diff --git a/DESCRIPTION b/DESCRIPTION
index 55f0808..e42d24d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: plinkQC
 Type: Package
 Title: Genotype Quality Control with 'PLINK'
-Version: 0.3.1
+Version: 0.3.2
 Authors@R:
     person("Hannah", "Meyer", email = "hannah.v.meyer@gmail.com",
     role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4564-0899"))
@@ -43,5 +43,5 @@ SystemRequirements:
     plink (1.9)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
index 41851a2..d8d8baa 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,46 +1,60 @@
+# plinkQC 0.3.2
+## minor changes
+* Add checks and tests in `evaluate_check_ancestry` for missing non-reference samples
+[5c03971](https://github.com/meyer-lab/plinkQC/commit/5c03971b92341b5a8cb26a1d5f2e37d637f5cbd7)
+* Clarified tutorials:
+  * R internal file.copy instead of systems `cp` command to make run on windows: [6c91ef3](https://github.com/meyer-lab/plinkQC/commit/6c91ef3368f601658967f88bc20db94a28307fce),
+  fixes [#26](https://github.com/meyer-lab/plinkQC/issues/26) 
+  * Add additional filter for A->T, C->G variants as suggested in [#24](https://github.com/meyer-lab/plinkQC/issues/24); [11e0375](https://github.com/meyer-lab/plinkQC/commit/11e03756852215915310a836d2e73dbcedf12bfc)
+* Fixed plotting issues in PCA plot of ancestry check:
+  * allow for supplying names of European reference population [ae09e64](https://github.com/meyer-lab/plinkQC/commit/ae09e64ee2eaeb8337b60b24b126a9c049d6315f)
+  * provide argument to specify number of populations per legend row [c7fe85d](https://github.com/meyer-lab/plinkQC/commit/c7fe85d555c256bf8be3843803ff1cc445f7898f)
+  * Ensure correct ordering of population colors when reference population is not HapMap [86275b7](https://github.com/meyer-lab/plinkQC/commit/86275b7c281835681f38ab16672db61c288cfed9)
+
 # plinkQC 0.3.1
 ## minor changes
-* Fixed dead links in vignettes (caused by migration of repository): da987d8f225aa6aca0596b9c4f6a2484b102bdb6
-* Added note about chrY in Hapmap data (vignette): e8afbb9842ed9421461a8114ac0a00f7955cf0c0
+
+* Fixed dead links in vignettes (caused by migration of repository): [da987d8](https://github.com/meyer-lab/plinkQC/commit/da987d8f225aa6aca0596b9c4f6a2484b102bdb6)
+* Added note about chrY in Hapmap data (vignette): [e8afbb9](https://github.com/meyer-lab/plinkQC/commit/e8afbb9842ed9421461a8114ac0a00f7955cf0c0)
 * Added note about recommended use of plink1.9 (vs 2.0):
-b69d3d71d23e9b161176a635fcb2b5a2b524591f
+[b69d3d7](https://github.com/meyer-lab/plinkQC/commit/b69d3d71d23e9b161176a635fcb2b5a2b524591f)
 
 # plinkQC 0.3.0
 ## major changes
 * Relationship filter can handle more complicated relationship scenarios as
-  observed in plant genotype sets (fixed #11)
+  observed in plant genotype sets (fixed [#11](https://github.com/meyer-lab/plinkQC/issues/11))
 * code moved to the meyer-lab repository: https://github.com/meyer-lab-cshl/plinkQC
 
 # plinkQC 0.2.3
 ## major changes
 * Enable return of overview plots as ggplot object
-  (fixes #6 in ab2e840f0f22ccdeb5317475698aa58e7eecd345 and
-  101e74e318752b2f8038330245d875f6afd5b57b)
+  (fixes  [#6](https://github.com/meyer-lab/plinkQC/issues/6) in [ab2e840](https://github.com/meyer-lab/plinkQC/commit/ab2e840f0f22ccdeb5317475698aa58e7eecd345) and
+  [101e74e](https://github.com/meyer-lab/plinkQC/commit/101e74e318752b2f8038330245d875f6afd5b57b))
 * Relationship filter now deals with more complicated relationship scenarios as
-  observed in plant genotype sets (fixed #11)
+  observed in plant genotype sets (addresses [#11](https://github.com/meyer-lab/plinkQC/issues/11))
 
 ## minor changes
 * give user option to choose maf threshold for relatedness filtering (relates to
-  #3)
+   [#3](https://github.com/meyer-lab/plinkQC/issues/3))
 
 ## bug fixes
-* Include check for zero related individuals fixing #3 in
-  1445a88d41d985e73ffdd161144229683f8352cd
+* Include check for zero related individuals fixing  [#3](https://github.com/meyer-lab/plinkQC/issues/3) in
+  [1445a88](https://github.com/meyer-lab/plinkQC/commit/1445a88d41d985e73ffdd161144229683f8352cd)
 * Include check in case all samples fail perIndividual QC in
-   894acc1fa03dadfe0ad2028888142171bcc641eb and
-   04642246d18ed4eaac5b9d9a6931d1ecb08308e8)
+   [894acc1](https://github.com/meyer-lab/plinkQC/commit/894acc1fa03dadfe0ad2028888142171bcc641eb) and
+   [0464224](https://github.com/meyer-lab/plinkQC/commit/04642246d18ed4eaac5b9d9a6931d1ecb08308e8))
 * Include checks for diagonal derived relationship estimates, and estimate data
-  containing only related individuals; fixes #11
+  containing only related individuals; addresses  [#11](https://github.com/meyer-lab/plinkQC/issues/11)
 * Fix command for genotype conversion in 1000Genomes vignette, addressing issue
-  #10
+   [#10](https://github.com/meyer-lab/plinkQC/issues/10)
 * fix missing rownames error for overviewPerIndividualQC, when relatedness check
-  was included (issue #16, fc7a38b1f2b345d9c6c5d69f5dcf0bc57a857f62)
-* fix vignette mismatch (issue #16, 09dcd59e77178b35747aae81a5c1988712e20de9)
+  was included (issue [#16](https://github.com/meyer-lab/plinkQC/issues/16), [fc7a38b](https://github.com/meyer-lab/plinkQC/commit/fc7a38b1f2b345d9c6c5d69f5dcf0bc57a857f62))
+* fix vignette mismatch (issue [#16](https://github.com/meyer-lab/plinkQC/issues/16), [09dcd59](https://github.com/meyer-lab/plinkQC/commit/09dcd59e77178b35747aae81a5c1988712e20de9))
 
 # plinkQC 0.2.2
 ## minor changes
 * Fix IDs written to fail.IDs file: previous versions wrote IID,IID, now fixed
-to FID, IID (fixes #2).
+to FID, IID (fixes [#2](https://github.com/meyer-lab/plinkQC/issues/2)).
 
 # plinkQC 0.2.1
 ## minor changes
diff --git a/R/individualQC.R b/R/individualQC.R
index e6c190e..68aae5e 100755
--- a/R/individualQC.R
+++ b/R/individualQC.R
@@ -916,11 +916,13 @@ check_relatedness <- function(indir, name, qcdir=indir, highIBDTh=0.1875,
 
 check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset,
                            europeanTh=1.5,
+                           refPopulation=c("CEU", "TSI"),
                            refSamples=NULL, refColors=NULL,
                            refSamplesFile=NULL, refColorsFile=NULL,
                            refSamplesIID="IID", refSamplesPop="Pop",
                            refColorsColor="Color", refColorsPop="Pop",
                            studyColor="#2c7bb6",
+                           legend_labels_per_row=6,
                            run.check_ancestry=TRUE,
                            interactive=FALSE, verbose=verbose,
                            path2plink=NULL, showPlinkOutput=TRUE) {
@@ -934,6 +936,7 @@ check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset,
         fail <- evaluate_check_ancestry(qcdir=qcdir, indir=indir, name=name,
                                         prefixMergedDataset=prefixMergedDataset,
                                         europeanTh=europeanTh,
+                                        refPopulation=refPopulation,
                                         refSamples=refSamples,
                                         refColors=refColors,
                                         refSamplesFile=refSamplesFile,
@@ -943,6 +946,7 @@ check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset,
                                         refColorsColor=refColorsColor,
                                         refColorsPop=refColorsPop,
                                         studyColor=studyColor,
+                                        legend_labels_per_row=legend_labels_per_row,
                                         interactive=interactive)
         return(fail)
 }
@@ -1789,6 +1793,9 @@ run_check_ancestry <- function(indir, prefixMergedDataset,
 #' considered to be of European descent and samples outside this radius of
 #' non-European descent. The radius is computed as the maximum Euclidean distance
 #' of European reference samples to the centre of European reference samples.
+#' @param refPopulation [vector] Vector with population identifiers of European
+#' reference population. Identifiers have to be corresponding to population IDs
+#' [refColorsPop] in refColorsfile/refColors.
 #' @param refSamples [data.frame] Dataframe with sample identifiers
 #' [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and
 #' population identifier [refSamplesPop] corresponding to population IDs
@@ -1820,6 +1827,7 @@ run_check_ancestry <- function(indir, prefixMergedDataset,
 #' IDs in refColors/refColorsFile.
 #' @param studyColor [character] Colour to be used for study population if plot
 #' is TRUE.
+#' @param legend_labels_per_row [integer] Number of population names per row in PCA plot.
 #' @param interactive [logical] Should plots be shown interactively? When
 #' choosing this option, make sure you have X-forwarding/graphical interface
 #' available for interactive plotting. Alternatively, set interactive=FALSE and
@@ -1849,6 +1857,8 @@ evaluate_check_ancestry <- function(indir, name, prefixMergedDataset,
                                     refSamplesIID="IID", refSamplesPop="Pop",
                                     refColorsColor="Color", refColorsPop="Pop",
                                     studyColor="#2c7bb6",
+                                    refPopulation=c("CEU", "TSI"),
+                                    legend_labels_per_row=6,
                                     interactive=FALSE) {
 
     prefix <- makepath(indir, name)
@@ -1866,11 +1876,20 @@ evaluate_check_ancestry <- function(indir, name, prefixMergedDataset,
     if (!file.exists(paste(out, ".eigenvec", sep=""))){
         stop("plink --pca output file: ", out, ".eigenvec does not exist.")
     }
-    testNumerics(numbers=europeanTh, positives=europeanTh)
+    testNumerics(numbers=c(europeanTh, legend_labels_per_row),
+                 positives=c(europeanTh, legend_labels_per_row))
     pca_data <- data.table::fread(paste(out, ".eigenvec", sep=""),
                                   stringsAsFactors=FALSE, data.table=FALSE)
     colnames(pca_data) <- c("FID", "IID", paste("PC",1:(ncol(pca_data)-2),
                                                 sep=""))
+    if (!any(samples$IID %in% pca_data$IID)) {
+        stop("There are no ", prefix, ".fam samples in the prefixMergedDataset")
+    }
+    if (!all(samples$IID %in% pca_data$IID)) {
+        stop("Not all ", prefix, ".fam samples are present in the",
+             "prefixMergedDataset")
+    }
+
     #pca_data$IID <- as.character(pca_data$IID)
     #pca_data$FID <- as.character(pca_data$FID)
 
@@ -1926,6 +1945,12 @@ evaluate_check_ancestry <- function(indir, name, prefixMergedDataset,
              refColors; missing population codes: ", paste(missing,
                                                            collapse=","))
     }
+    if (!all(refPopulation %in% refColors$Pop)) {
+        missing <- refPopulation[!refPopulation %in% refColors$Pop]
+        stop("Not all refPopulation populations found in population code of
+             refColors; missing population codes: ", paste(missing,
+                                                           collapse=","))
+    }
     refSamples <- merge(refSamples, refColors, by="Pop", all.X=TRUE)
 
     ## Combine pca data and population information ####
@@ -1936,14 +1961,15 @@ evaluate_check_ancestry <- function(indir, name, prefixMergedDataset,
         stop("There are samples in the prefixMergedDataset that cannot be found
              in refSamples or ", prefix, ".fam")
     }
-    data_all <- data_all[order(data_all$Pop, decreasing=FALSE),]
 
-    refColors <- rbind(refColors, c(name, studyColor))
-    data_all$Color <- as.factor(data_all$Color)
-    data_all$Pop <- factor(data_all$Pop, levels=refColors$Pop)
+    colors <-  dplyr::select_(data_all, ~Pop, ~Color)
+    colors <- colors[!duplicated(colors$Pop),]
+    colors <- colors[order(colors$Color),]
+    colors$Pop <- factor(colors$Pop, levels=unique(colors$Pop))
+    data_all$Pop <- factor(data_all$Pop, levels=levels(colors$Pop))
 
     ## Find mean coordinates and distances of reference Europeans ####
-    all_european <- dplyr::filter_(data_all, ~Pop %in% c("CEU", "TSI"))
+    all_european <- dplyr::filter_(data_all, ~Pop %in% refPopulation)
     euro_pc1_mean <- mean(all_european$PC1)
     euro_pc2_mean <- mean(all_european$PC2)
 
@@ -1959,17 +1985,17 @@ evaluate_check_ancestry <- function(indir, name, prefixMergedDataset,
     non_europeans <- dplyr::filter_(data_name, ~euclid_dist >
                                         (max_euclid_dist * europeanTh))
     fail_ancestry <- dplyr::select_(non_europeans, ~FID, ~IID)
+    legend_rows <- round(nrow(colors)/legend_labels_per_row)
     p_ancestry <- ggplot()
-    p_ancestry <- p_ancestry + geom_point(data=data_all,
-                                          aes_string(x='PC1', y='PC2',
-                                                     color='Pop')) +
+    p_ancestry <- p_ancestry +
+        geom_point(data=data_all,
+                   aes_string(x='PC1', y='PC2', color='Pop')) +
         geom_point(data=dplyr::filter_(data_all, ~Pop != name),
-                   aes_string(x='PC1', y='PC2',
-                              color='Pop'),
+                   aes_string(x='PC1', y='PC2', color='Pop'),
                    size=1) +
-        scale_color_manual(values=refColors$Color,
+        scale_color_manual(values=colors$Color,
                            name="Population") +
-        guides(color=guide_legend(nrow=2, byrow=TRUE)) +
+        guides(color=guide_legend(nrow=legend_rows, byrow=TRUE)) +
         ggforce::geom_circle(aes(x0=euro_pc1_mean, y0=euro_pc2_mean,
                                  r=(max_euclid_dist * europeanTh))) +
         ggtitle("PCA on combined reference and study genotypes") +
diff --git a/inst/extdata/data.fail-IBD.IDs b/inst/extdata/data.fail-IBD.IDs
deleted file mode 100644
index d09a39e..0000000
--- a/inst/extdata/data.fail-IBD.IDs
+++ /dev/null
@@ -1,14 +0,0 @@
-FID	IID
-ID_162	ID_162
-ID_167	ID_167
-ID_168	ID_168
-ID_155	ID_155
-ID_159	ID_159
-ID_156	ID_156
-ID_157	ID_157
-ID_158	ID_158
-ID_160	ID_160
-ID_161	ID_161
-ID_152	ID_152
-ID_153	ID_153
-ID_154	ID_154
diff --git a/man/check_ancestry.Rd b/man/check_ancestry.Rd
index 507f676..5f440a6 100644
--- a/man/check_ancestry.Rd
+++ b/man/check_ancestry.Rd
@@ -4,13 +4,29 @@
 \alias{check_ancestry}
 \title{Identification of individuals of divergent ancestry}
 \usage{
-check_ancestry(indir, name, qcdir = indir, prefixMergedDataset,
-  europeanTh = 1.5, refSamples = NULL, refColors = NULL,
-  refSamplesFile = NULL, refColorsFile = NULL, refSamplesIID = "IID",
-  refSamplesPop = "Pop", refColorsColor = "Color",
-  refColorsPop = "Pop", studyColor = "#2c7bb6",
-  run.check_ancestry = TRUE, interactive = FALSE, verbose = verbose,
-  path2plink = NULL, showPlinkOutput = TRUE)
+check_ancestry(
+  indir,
+  name,
+  qcdir = indir,
+  prefixMergedDataset,
+  europeanTh = 1.5,
+  refPopulation = c("CEU", "TSI"),
+  refSamples = NULL,
+  refColors = NULL,
+  refSamplesFile = NULL,
+  refColorsFile = NULL,
+  refSamplesIID = "IID",
+  refSamplesPop = "Pop",
+  refColorsColor = "Color",
+  refColorsPop = "Pop",
+  studyColor = "#2c7bb6",
+  legend_labels_per_row = 6,
+  run.check_ancestry = TRUE,
+  interactive = FALSE,
+  verbose = verbose,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
@@ -37,6 +53,10 @@ non-European descent. The radius is computed as the maximum Euclidean
 distance of European reference samples to the centre of European reference
 samples.}
 
+\item{refPopulation}{[vector] Vector with population identifiers of European
+reference population. Identifiers have to be corresponding to population IDs
+[refColorsPop] in refColorsfile/refColors.}
+
 \item{refSamples}{[data.frame] Dataframe with sample identifiers
 [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and
 population identifier [refSamplesPop] corresponding to population IDs
@@ -73,6 +93,8 @@ IDs in refColors/refColorsFile.}
 
 \item{studyColor}{[character] Colour to be used for study population.}
 
+\item{legend_labels_per_row}{[integer] Number of population names per row in PCA plot.}
+
 \item{run.check_ancestry}{[logical] Should plink --pca be run to
 determine principal components of merged dataset; if FALSE, it is assumed
 that plink --pca has been run successfully and
diff --git a/man/check_het_and_miss.Rd b/man/check_het_and_miss.Rd
index d6a87ab..db93ad0 100644
--- a/man/check_het_and_miss.Rd
+++ b/man/check_het_and_miss.Rd
@@ -5,10 +5,19 @@
 \title{Identification of individuals with outlying missing genotype or
 heterozygosity rates}
 \usage{
-check_het_and_miss(indir, name, qcdir = indir, imissTh = 0.03,
-  hetTh = 3, run.check_het_and_miss = TRUE, label = TRUE,
-  interactive = FALSE, verbose = FALSE, path2plink = NULL,
-  showPlinkOutput = TRUE)
+check_het_and_miss(
+  indir,
+  name,
+  qcdir = indir,
+  imissTh = 0.03,
+  hetTh = 3,
+  run.check_het_and_miss = TRUE,
+  label = TRUE,
+  interactive = FALSE,
+  verbose = FALSE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/check_hwe.Rd b/man/check_hwe.Rd
index fece4eb..f3e6324 100644
--- a/man/check_hwe.Rd
+++ b/man/check_hwe.Rd
@@ -5,9 +5,16 @@
 \title{Identification of SNPs showing a significant deviation from Hardy-Weinberg-
 equilibrium (HWE)}
 \usage{
-check_hwe(indir, name, qcdir = indir, hweTh = 1e-05,
-  interactive = FALSE, path2plink = NULL, verbose = FALSE,
-  showPlinkOutput = TRUE)
+check_hwe(
+  indir,
+  name,
+  qcdir = indir,
+  hweTh = 1e-05,
+  interactive = FALSE,
+  path2plink = NULL,
+  verbose = FALSE,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/check_maf.Rd b/man/check_maf.Rd
index 60e1172..609e1f3 100644
--- a/man/check_maf.Rd
+++ b/man/check_maf.Rd
@@ -4,9 +4,17 @@
 \alias{check_maf}
 \title{Identification of SNPs with low minor allele frequency}
 \usage{
-check_maf(indir, name, qcdir = indir, macTh = 20, mafTh = NULL,
-  verbose = FALSE, interactive = FALSE, path2plink = NULL,
-  showPlinkOutput = TRUE)
+check_maf(
+  indir,
+  name,
+  qcdir = indir,
+  macTh = 20,
+  mafTh = NULL,
+  verbose = FALSE,
+  interactive = FALSE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/check_relatedness.Rd b/man/check_relatedness.Rd
index a2a6b35..99bb945 100644
--- a/man/check_relatedness.Rd
+++ b/man/check_relatedness.Rd
@@ -4,10 +4,20 @@
 \alias{check_relatedness}
 \title{Identification of related individuals}
 \usage{
-check_relatedness(indir, name, qcdir = indir, highIBDTh = 0.1875,
-  genomebuild = "hg19", imissTh = 0.03, run.check_relatedness = TRUE,
-  interactive = FALSE, verbose = FALSE, mafThRelatedness = 0.1,
-  path2plink = NULL, showPlinkOutput = TRUE)
+check_relatedness(
+  indir,
+  name,
+  qcdir = indir,
+  highIBDTh = 0.1875,
+  genomebuild = "hg19",
+  imissTh = 0.03,
+  run.check_relatedness = TRUE,
+  interactive = FALSE,
+  verbose = FALSE,
+  mafThRelatedness = 0.1,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/check_sex.Rd b/man/check_sex.Rd
index 82c4664..9420e52 100644
--- a/man/check_sex.Rd
+++ b/man/check_sex.Rd
@@ -4,11 +4,25 @@
 \alias{check_sex}
 \title{Identification of individuals with discordant sex information}
 \usage{
-check_sex(indir, name, qcdir = indir, maleTh = 0.8, femaleTh = 0.2,
-  run.check_sex = TRUE, externalSex = NULL, externalFemale = "F",
-  externalMale = "M", externalSexSex = "Sex", externalSexID = "IID",
-  fixMixup = FALSE, interactive = FALSE, verbose = FALSE,
-  label = TRUE, path2plink = NULL, showPlinkOutput = TRUE)
+check_sex(
+  indir,
+  name,
+  qcdir = indir,
+  maleTh = 0.8,
+  femaleTh = 0.2,
+  run.check_sex = TRUE,
+  externalSex = NULL,
+  externalFemale = "F",
+  externalMale = "M",
+  externalSexSex = "Sex",
+  externalSexID = "IID",
+  fixMixup = FALSE,
+  interactive = FALSE,
+  verbose = FALSE,
+  label = TRUE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/check_snp_missingness.Rd b/man/check_snp_missingness.Rd
index 77ff950..5cc89db 100644
--- a/man/check_snp_missingness.Rd
+++ b/man/check_snp_missingness.Rd
@@ -4,9 +4,16 @@
 \alias{check_snp_missingness}
 \title{Identification of SNPs with high missingness rate}
 \usage{
-check_snp_missingness(indir, name, qcdir = indir, lmissTh = 0.01,
-  interactive = FALSE, path2plink = NULL, verbose = FALSE,
-  showPlinkOutput = TRUE)
+check_snp_missingness(
+  indir,
+  name,
+  qcdir = indir,
+  lmissTh = 0.01,
+  interactive = FALSE,
+  path2plink = NULL,
+  verbose = FALSE,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/cleanData.Rd b/man/cleanData.Rd
index f7691b7..2ebd572 100644
--- a/man/cleanData.Rd
+++ b/man/cleanData.Rd
@@ -4,12 +4,26 @@
 \alias{cleanData}
 \title{Create plink dataset with individuals and markers passing quality control}
 \usage{
-cleanData(indir, name, qcdir = indir, filterSex = TRUE,
-  filterHeterozygosity = TRUE, filterSampleMissingness = TRUE,
-  filterAncestry = TRUE, filterRelated = TRUE,
-  filterSNPMissingness = TRUE, lmissTh = 0.01, filterHWE = TRUE,
-  hweTh = 1e-05, filterMAF = TRUE, macTh = 20, mafTh = NULL,
-  path2plink = NULL, verbose = FALSE, showPlinkOutput = TRUE)
+cleanData(
+  indir,
+  name,
+  qcdir = indir,
+  filterSex = TRUE,
+  filterHeterozygosity = TRUE,
+  filterSampleMissingness = TRUE,
+  filterAncestry = TRUE,
+  filterRelated = TRUE,
+  filterSNPMissingness = TRUE,
+  lmissTh = 0.01,
+  filterHWE = TRUE,
+  hweTh = 1e-05,
+  filterMAF = TRUE,
+  macTh = 20,
+  mafTh = NULL,
+  path2plink = NULL,
+  verbose = FALSE,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/evaluate_check_ancestry.Rd b/man/evaluate_check_ancestry.Rd
index 24db6b5..70919d7 100644
--- a/man/evaluate_check_ancestry.Rd
+++ b/man/evaluate_check_ancestry.Rd
@@ -4,11 +4,25 @@
 \alias{evaluate_check_ancestry}
 \title{Evaluate results from PLINK PCA on combined study and reference data}
 \usage{
-evaluate_check_ancestry(indir, name, prefixMergedDataset, qcdir = indir,
-  europeanTh = 1.5, refSamples = NULL, refColors = NULL,
-  refSamplesFile = NULL, refColorsFile = NULL, refSamplesIID = "IID",
-  refSamplesPop = "Pop", refColorsColor = "Color",
-  refColorsPop = "Pop", studyColor = "#2c7bb6", interactive = FALSE)
+evaluate_check_ancestry(
+  indir,
+  name,
+  prefixMergedDataset,
+  qcdir = indir,
+  europeanTh = 1.5,
+  refSamples = NULL,
+  refColors = NULL,
+  refSamplesFile = NULL,
+  refColorsFile = NULL,
+  refSamplesIID = "IID",
+  refSamplesPop = "Pop",
+  refColorsColor = "Color",
+  refColorsPop = "Pop",
+  studyColor = "#2c7bb6",
+  refPopulation = c("CEU", "TSI"),
+  legend_labels_per_row = 6,
+  interactive = FALSE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
@@ -71,6 +85,12 @@ IDs in refColors/refColorsFile.}
 \item{studyColor}{[character] Colour to be used for study population if plot
 is TRUE.}
 
+\item{refPopulation}{[vector] Vector with population identifiers of European
+reference population. Identifiers have to be corresponding to population IDs
+[refColorsPop] in refColorsfile/refColors.}
+
+\item{legend_labels_per_row}{[integer] Number of population names per row in PCA plot.}
+
 \item{interactive}{[logical] Should plots be shown interactively? When
 choosing this option, make sure you have X-forwarding/graphical interface
 available for interactive plotting. Alternatively, set interactive=FALSE and
diff --git a/man/evaluate_check_het_and_miss.Rd b/man/evaluate_check_het_and_miss.Rd
index 0d8b74e..7d3900d 100644
--- a/man/evaluate_check_het_and_miss.Rd
+++ b/man/evaluate_check_het_and_miss.Rd
@@ -4,8 +4,14 @@
 \alias{evaluate_check_het_and_miss}
 \title{Evaluate results from PLINK missing genotype and heterozygosity rate check.}
 \usage{
-evaluate_check_het_and_miss(qcdir, name, imissTh = 0.03, hetTh = 3,
-  label = TRUE, interactive = FALSE)
+evaluate_check_het_and_miss(
+  qcdir,
+  name,
+  imissTh = 0.03,
+  hetTh = 3,
+  label = TRUE,
+  interactive = FALSE
+)
 }
 \arguments{
 \item{qcdir}{[character] path/to/directory/with/QC/results containing
diff --git a/man/evaluate_check_relatedness.Rd b/man/evaluate_check_relatedness.Rd
index 02a6914..c81cb9a 100644
--- a/man/evaluate_check_relatedness.Rd
+++ b/man/evaluate_check_relatedness.Rd
@@ -4,8 +4,14 @@
 \alias{evaluate_check_relatedness}
 \title{Evaluate results from PLINK IBD estimation.}
 \usage{
-evaluate_check_relatedness(qcdir, name, highIBDTh = 0.1875,
-  imissTh = 0.03, interactive = FALSE, verbose = FALSE)
+evaluate_check_relatedness(
+  qcdir,
+  name,
+  highIBDTh = 0.1875,
+  imissTh = 0.03,
+  interactive = FALSE,
+  verbose = FALSE
+)
 }
 \arguments{
 \item{qcdir}{[character] path/to/directory/with/QC/results containing
diff --git a/man/evaluate_check_sex.Rd b/man/evaluate_check_sex.Rd
index 7532131..8da7e8c 100644
--- a/man/evaluate_check_sex.Rd
+++ b/man/evaluate_check_sex.Rd
@@ -4,11 +4,24 @@
 \alias{evaluate_check_sex}
 \title{Evaluate results from PLINK sex check.}
 \usage{
-evaluate_check_sex(qcdir, name, maleTh = 0.8, femaleTh = 0.2,
-  externalSex = NULL, fixMixup = FALSE, indir = qcdir,
-  externalFemale = "F", externalMale = "M", externalSexSex = "Sex",
-  externalSexID = "IID", verbose = FALSE, label = TRUE,
-  path2plink = NULL, showPlinkOutput = TRUE, interactive = FALSE)
+evaluate_check_sex(
+  qcdir,
+  name,
+  maleTh = 0.8,
+  femaleTh = 0.2,
+  externalSex = NULL,
+  fixMixup = FALSE,
+  indir = qcdir,
+  externalFemale = "F",
+  externalMale = "M",
+  externalSexSex = "Sex",
+  externalSexID = "IID",
+  verbose = FALSE,
+  label = TRUE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE,
+  interactive = FALSE
+)
 }
 \arguments{
 \item{qcdir}{[character] /path/to/directory containing name.sexcheck as
diff --git a/man/perIndividualQC.Rd b/man/perIndividualQC.Rd
index 310626d..13aeccc 100644
--- a/man/perIndividualQC.Rd
+++ b/man/perIndividualQC.Rd
@@ -4,24 +4,52 @@
 \alias{perIndividualQC}
 \title{Quality control for all individuals in plink-dataset}
 \usage{
-perIndividualQC(indir, name, qcdir = indir, dont.check_sex = FALSE,
-  do.run_check_sex = TRUE, do.evaluate_check_sex = TRUE,
-  maleTh = 0.8, femaleTh = 0.2, externalSex = NULL,
-  externalMale = "M", externalSexSex = "Sex", externalSexID = "IID",
-  externalFemale = "F", fixMixup = FALSE,
-  dont.check_het_and_miss = FALSE, do.run_check_het_and_miss = TRUE,
-  do.evaluate_check_het_and_miss = TRUE, imissTh = 0.03, hetTh = 3,
-  dont.check_relatedness = FALSE, do.run_check_relatedness = TRUE,
-  do.evaluate_check_relatedness = TRUE, highIBDTh = 0.1875,
-  mafThRelatedness = 0.1, genomebuild = "hg19",
-  dont.check_ancestry = FALSE, do.run_check_ancestry = TRUE,
-  do.evaluate_check_ancestry = TRUE, prefixMergedDataset,
-  europeanTh = 1.5, refSamples = NULL, refColors = NULL,
-  refSamplesFile = NULL, refColorsFile = NULL, refSamplesIID = "IID",
-  refSamplesPop = "Pop", refColorsColor = "Color",
-  refColorsPop = "Pop", studyColor = "#2c7bb6", label = TRUE,
-  interactive = FALSE, verbose = TRUE, path2plink = NULL,
-  showPlinkOutput = TRUE)
+perIndividualQC(
+  indir,
+  name,
+  qcdir = indir,
+  dont.check_sex = FALSE,
+  do.run_check_sex = TRUE,
+  do.evaluate_check_sex = TRUE,
+  maleTh = 0.8,
+  femaleTh = 0.2,
+  externalSex = NULL,
+  externalMale = "M",
+  externalSexSex = "Sex",
+  externalSexID = "IID",
+  externalFemale = "F",
+  fixMixup = FALSE,
+  dont.check_het_and_miss = FALSE,
+  do.run_check_het_and_miss = TRUE,
+  do.evaluate_check_het_and_miss = TRUE,
+  imissTh = 0.03,
+  hetTh = 3,
+  dont.check_relatedness = FALSE,
+  do.run_check_relatedness = TRUE,
+  do.evaluate_check_relatedness = TRUE,
+  highIBDTh = 0.1875,
+  mafThRelatedness = 0.1,
+  genomebuild = "hg19",
+  dont.check_ancestry = FALSE,
+  do.run_check_ancestry = TRUE,
+  do.evaluate_check_ancestry = TRUE,
+  prefixMergedDataset,
+  europeanTh = 1.5,
+  refSamples = NULL,
+  refColors = NULL,
+  refSamplesFile = NULL,
+  refColorsFile = NULL,
+  refSamplesIID = "IID",
+  refSamplesPop = "Pop",
+  refColorsColor = "Color",
+  refColorsPop = "Pop",
+  studyColor = "#2c7bb6",
+  label = TRUE,
+  interactive = FALSE,
+  verbose = TRUE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/perMarkerQC.Rd b/man/perMarkerQC.Rd
index 4a129b5..74f2c1b 100644
--- a/man/perMarkerQC.Rd
+++ b/man/perMarkerQC.Rd
@@ -4,11 +4,22 @@
 \alias{perMarkerQC}
 \title{Quality control for all markers in plink-dataset}
 \usage{
-perMarkerQC(indir, qcdir = indir, name,
-  do.check_snp_missingness = TRUE, lmissTh = 0.01,
-  do.check_hwe = TRUE, hweTh = 1e-05, do.check_maf = TRUE,
-  macTh = 20, mafTh = NULL, interactive = FALSE, verbose = TRUE,
-  path2plink = NULL, showPlinkOutput = TRUE)
+perMarkerQC(
+  indir,
+  qcdir = indir,
+  name,
+  do.check_snp_missingness = TRUE,
+  lmissTh = 0.01,
+  do.check_hwe = TRUE,
+  hweTh = 1e-05,
+  do.check_maf = TRUE,
+  macTh = 20,
+  mafTh = NULL,
+  interactive = FALSE,
+  verbose = TRUE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/plinkQC.Rd b/man/plinkQC.Rd
index 12121f2..acba21b 100644
--- a/man/plinkQC.Rd
+++ b/man/plinkQC.Rd
@@ -3,9 +3,5 @@
 \docType{package}
 \name{plinkQC}
 \alias{plinkQC}
-\alias{plinkQC-package}
 \title{plinkQC}
-\description{
-plinkQC
-}
 \keyword{internal}
diff --git a/man/relatednessFilter.Rd b/man/relatednessFilter.Rd
index 9c0e989..a22a5b9 100644
--- a/man/relatednessFilter.Rd
+++ b/man/relatednessFilter.Rd
@@ -4,13 +4,21 @@
 \alias{relatednessFilter}
 \title{Remove related individuals while keeping maximum number of individuals}
 \usage{
-relatednessFilter(relatedness, otherCriterion = NULL, relatednessTh,
-  otherCriterionTh = NULL, otherCriterionThDirection = c("gt", "ge",
-  "lt", "le", "eq"), relatednessIID1 = "IID1",
-  relatednessIID2 = "IID2", relatednessFID1 = NULL,
-  relatednessFID2 = NULL, relatednessRelatedness = "PI_HAT",
-  otherCriterionIID = "IID", otherCriterionMeasure = NULL,
-  verbose = FALSE)
+relatednessFilter(
+  relatedness,
+  otherCriterion = NULL,
+  relatednessTh,
+  otherCriterionTh = NULL,
+  otherCriterionThDirection = c("gt", "ge", "lt", "le", "eq"),
+  relatednessIID1 = "IID1",
+  relatednessIID2 = "IID2",
+  relatednessFID1 = NULL,
+  relatednessFID2 = NULL,
+  relatednessRelatedness = "PI_HAT",
+  otherCriterionIID = "IID",
+  otherCriterionMeasure = NULL,
+  verbose = FALSE
+)
 }
 \arguments{
 \item{relatedness}{[data.frame] containing pair-wise relatedness estimates
diff --git a/man/run_check_ancestry.Rd b/man/run_check_ancestry.Rd
index 8b792c8..b916df9 100644
--- a/man/run_check_ancestry.Rd
+++ b/man/run_check_ancestry.Rd
@@ -4,8 +4,14 @@
 \alias{run_check_ancestry}
 \title{Run PLINK principal component analysis}
 \usage{
-run_check_ancestry(indir, prefixMergedDataset, qcdir = indir,
-  verbose = FALSE, path2plink = NULL, showPlinkOutput = TRUE)
+run_check_ancestry(
+  indir,
+  prefixMergedDataset,
+  qcdir = indir,
+  verbose = FALSE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/run_check_heterozygosity.Rd b/man/run_check_heterozygosity.Rd
index 3d57cc6..d8c2b72 100644
--- a/man/run_check_heterozygosity.Rd
+++ b/man/run_check_heterozygosity.Rd
@@ -4,8 +4,14 @@
 \alias{run_check_heterozygosity}
 \title{Run PLINK heterozygosity rate calculation}
 \usage{
-run_check_heterozygosity(indir, name, qcdir = indir, verbose = FALSE,
-  path2plink = NULL, showPlinkOutput = TRUE)
+run_check_heterozygosity(
+  indir,
+  name,
+  qcdir = indir,
+  verbose = FALSE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/run_check_missingness.Rd b/man/run_check_missingness.Rd
index 159d50a..74a471f 100644
--- a/man/run_check_missingness.Rd
+++ b/man/run_check_missingness.Rd
@@ -4,8 +4,14 @@
 \alias{run_check_missingness}
 \title{Run PLINK missingness rate calculation}
 \usage{
-run_check_missingness(indir, name, qcdir = indir, verbose = FALSE,
-  path2plink = NULL, showPlinkOutput = TRUE)
+run_check_missingness(
+  indir,
+  name,
+  qcdir = indir,
+  verbose = FALSE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/run_check_relatedness.Rd b/man/run_check_relatedness.Rd
index cf93ac7..b6ead12 100644
--- a/man/run_check_relatedness.Rd
+++ b/man/run_check_relatedness.Rd
@@ -4,9 +4,17 @@
 \alias{run_check_relatedness}
 \title{Run PLINK IBD estimation}
 \usage{
-run_check_relatedness(indir, name, qcdir = indir, highIBDTh = 0.185,
-  mafThRelatedness = 0.1, path2plink = NULL, genomebuild = "hg19",
-  showPlinkOutput = TRUE, verbose = FALSE)
+run_check_relatedness(
+  indir,
+  name,
+  qcdir = indir,
+  highIBDTh = 0.185,
+  mafThRelatedness = 0.1,
+  path2plink = NULL,
+  genomebuild = "hg19",
+  showPlinkOutput = TRUE,
+  verbose = FALSE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/run_check_sex.Rd b/man/run_check_sex.Rd
index bf3d5c3..d398c83 100644
--- a/man/run_check_sex.Rd
+++ b/man/run_check_sex.Rd
@@ -4,8 +4,14 @@
 \alias{run_check_sex}
 \title{Run PLINK sexcheck}
 \usage{
-run_check_sex(indir, name, qcdir = indir, verbose = FALSE,
-  path2plink = NULL, showPlinkOutput = TRUE)
+run_check_sex(
+  indir,
+  name,
+  qcdir = indir,
+  verbose = FALSE,
+  path2plink = NULL,
+  showPlinkOutput = TRUE
+)
 }
 \arguments{
 \item{indir}{[character] /path/to/directory containing the basic PLINK data
diff --git a/man/testNumerics.Rd b/man/testNumerics.Rd
index 14d7293..d8a9f6c 100644
--- a/man/testNumerics.Rd
+++ b/man/testNumerics.Rd
@@ -4,8 +4,7 @@
 \alias{testNumerics}
 \title{Test lists for different properties of numerics}
 \usage{
-testNumerics(numbers, positives = NULL, integers = NULL,
-  proportions = NULL)
+testNumerics(numbers, positives = NULL, integers = NULL, proportions = NULL)
 }
 \arguments{
 \item{numbers}{[list] whose elements are tested for being numeric.}
diff --git a/tests/testthat/data.HapMapIII_no_samples.eigenvec b/tests/testthat/data.HapMapIII_no_samples.eigenvec
new file mode 100644
index 0000000..b189934
--- /dev/null
+++ b/tests/testthat/data.HapMapIII_no_samples.eigenvec
@@ -0,0 +1,1184 @@
+1328 NA06984 0.0112364 -0.0131228
+1328 NA06989 0.011215 -0.012809
+1330 NA12335 0.0111011 -0.0133978
+1330 NA12336 0.0111579 -0.0135819
+1330 NA12340 0.0113226 -0.0135114
+1330 NA12341 0.0106949 -0.0132038
+1330 NA12342 0.0115182 -0.013525
+1330 NA12343 0.0112338 -0.0127326
+1334 NA10846 0.0112211 -0.0134252
+1334 NA10847 0.011217 -0.0135979
+1334 NA12144 0.0111611 -0.0130571
+1334 NA12145 0.0111979 -0.0140401
+1334 NA12146 0.0109181 -0.0138649
+1334 NA12239 0.0113968 -0.013171
+1340 NA06994 0.0109126 -0.0124034
+1340 NA07000 0.0112091 -0.0127042
+1340 NA07022 0.0108527 -0.0127343
+1340 NA07029 0.0112237 -0.0125226
+1340 NA07056 0.0112648 -0.012908
+1341 NA06985 0.00996875 -0.0127817
+1341 NA06991 0.0110227 -0.012901
+1341 NA06993 0.0111939 -0.0129679
+1341 NA07055 0.0112207 -0.0130248
+1344 NA10850 0.0113347 -0.0132881
+1344 NA12056 0.0113973 -0.013498
+1344 NA12057 0.0110258 -0.0128913
+1345 NA07345 0.0111624 -0.0131538
+1345 NA07346 0.0115168 -0.0127935
+1345 NA07347 0.0112581 -0.0135068
+1345 NA07348 0.0113013 -0.0135438
+1345 NA07349 0.0113276 -0.0127988
+1345 NA07357 0.0113302 -0.0135404
+1346 NA10852 0.011209 -0.0132409
+1346 NA12043 0.0115969 -0.0132339
+1346 NA12044 0.011445 -0.0127184
+1346 NA12045 0.0112533 -0.0127857
+1347 NA10859 0.0111602 -0.0130235
+1347 NA11881 0.0111384 -0.0128235
+1347 NA11882 0.0111565 -0.0131035
+1349 NA10853 0.0112834 -0.0133026
+1349 NA10854 0.0110971 -0.0125596
+1349 NA11839 0.011205 -0.0129353
+1349 NA11840 0.0100352 -0.012356
+1349 NA11843 0.011212 -0.0135631
+1350 NA10855 0.0107867 -0.013526
+1350 NA10856 0.0112001 -0.0129608
+1350 NA11829 0.011385 -0.0131551
+1350 NA11830 0.0115351 -0.0128352
+1350 NA11831 0.0111177 -0.0132344
+1350 NA11832 0.0110522 -0.0133852
+1353 NA12375 0.0109243 -0.0131913
+1353 NA12376 0.0111172 -0.0135926
+1353 NA12383 0.0109685 -0.0131495
+1353 NA12489 0.0112424 -0.0135034
+1353 NA12546 0.0112103 -0.0127052
+1354 NA12386 0.0113198 -0.0131715
+1354 NA12399 0.0113557 -0.0134936
+1354 NA12400 0.0114199 -0.0131987
+1355 NA12413 0.0110739 -0.0127862
+1358 NA12707 0.0110629 -0.0134217
+1358 NA12708 0.0113285 -0.0127009
+1358 NA12716 0.0113984 -0.0141307
+1358 NA12718 0.0112379 -0.0128622
+1362 NA10861 0.0111415 -0.0133034
+1362 NA11992 0.0109893 -0.0132594
+1362 NA11993 0.0108506 -0.0133715
+1362 NA11994 0.0113475 -0.0129526
+1362 NA11995 0.0113 -0.0135651
+1375 NA10863 0.0113854 -0.0131805
+1375 NA12234 0.0113272 -0.0129669
+1375 NA12264 0.011375 -0.013192
+1377 NA10864 0.011342 -0.0130721
+1377 NA10865 0.0114637 -0.0127127
+1377 NA11891 0.0114619 -0.0131681
+1377 NA11892 0.0113004 -0.0124083
+1377 NA11893 0.0114424 -0.012992
+1377 NA11894 0.0112772 -0.0134659
+1408 NA10830 0.0115076 -0.0130928
+1408 NA10831 0.0113743 -0.0132619
+1408 NA12154 0.0114851 -0.0127687
+1408 NA12155 0.0114788 -0.0134849
+1408 NA12156 0.0108822 -0.0133196
+1416 NA10835 0.0115735 -0.0127982
+1416 NA12248 0.0112451 -0.0129779
+1416 NA12249 0.0116918 -0.0127581
+1418 NA10836 0.0112166 -0.0137516
+1418 NA10837 0.0111641 -0.0127194
+1418 NA12272 0.0113784 -0.0131899
+1418 NA12273 0.0109299 -0.0131688
+1418 NA12275 0.0112744 -0.0135621
+1420 NA10838 0.0111883 -0.0126795
+1420 NA10839 0.01142 -0.0137763
+1420 NA12003 0.0103997 -0.0124766
+1420 NA12005 0.0115508 -0.0134526
+1420 NA12006 0.0114584 -0.0134718
+1421 NA10840 0.0112512 -0.0125693
+1421 NA12282 0.01057 -0.0121887
+1421 NA12283 0.0106747 -0.0127711
+1421 NA12286 0.010894 -0.011949
+1421 NA12287 0.011172 -0.0129705
+1423 NA10843 0.0113695 -0.0135625
+1423 NA11917 0.0109498 -0.0121302
+1423 NA11918 0.0114404 -0.0125972
+1423 NA11919 0.0113091 -0.0133039
+1423 NA11920 0.0115254 -0.0134742
+1424 NA10845 0.0112541 -0.0132266
+1424 NA11930 0.0112836 -0.0128274
+1424 NA11931 0.0114488 -0.0133909
+1444 NA12739 0.0115596 -0.0131464
+1444 NA12740 0.0112946 -0.0130317
+1444 NA12748 0.0114936 -0.0125219
+1444 NA12749 0.011381 -0.0133384
+1444 NA12750 0.0112475 -0.0129569
+1444 NA12751 0.0113139 -0.0137146
+1447 NA12752 0.0112962 -0.0131305
+1447 NA12753 0.0112435 -0.0129118
+1447 NA12760 0.0109577 -0.0131923
+1447 NA12761 0.01134 -0.0129194
+1447 NA12762 0.0114367 -0.0130691
+1447 NA12763 0.0111486 -0.0129423
+1451 NA12766 0.0117072 -0.0131584
+1451 NA12767 0.0118209 -0.0134336
+1451 NA12775 0.0117358 -0.0132678
+1451 NA12776 0.0113573 -0.012977
+1451 NA12777 0.0116156 -0.0132723
+1451 NA12778 0.0116339 -0.0133329
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diff --git a/tests/testthat/data.HapMapIII_some_samples.eigenvec b/tests/testthat/data.HapMapIII_some_samples.eigenvec
new file mode 100644
index 0000000..1710e2b
--- /dev/null
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diff --git a/tests/testthat/test-individualQC.R b/tests/testthat/test-individualQC.R
index 2f43d24..0dd6236 100644
--- a/tests/testthat/test-individualQC.R
+++ b/tests/testthat/test-individualQC.R
@@ -194,11 +194,20 @@ test_that('evaluate_check_ancestry throws missing population code error',{
                  "Not all refSamples populations")
 })
 
+test_that('evaluate_check_ancestry throws missing refPopulation code error',{
+    expect_error(evaluate_check_ancestry(qcdir, name,
+                                         prefixMergedDataset=prefix,
+                                         refSamples=refSamples,
+                                         refPopulation = c("CCC")),
+                 "Not all refPopulation populations")
+})
+
 test_that('evaluate_check_ancestry throws missing missing ID error',{
-    testRefs <- refSamples[1:4,]
+    testRefs <- refSamples[84:88,]
     expect_error(evaluate_check_ancestry(qcdir, name,
                                          prefixMergedDataset=prefix,
-                                         refSamples=testRefs),
+                                         refSamples=testRefs,
+                                         refPopulation = "CEU"),
                  "There are samples in the prefixMergedDataset")
 })
 
@@ -234,3 +243,16 @@ test_that('evaluate_check_ancestry returns correct fail IDs for example data',{
     expect_true(all(fail$fail_ancestry$IID %in% fail_ancestryIDs[,1]))
 })
 
+test_that('evaluate_check_ancestry fails with all missing sample error',{
+    expect_error(evaluate_check_ancestry(
+        qcdir, name, prefixMergedDataset="data.HapMapIII_no_samples",
+        refSamples=refSamples),
+        "There are no")
+})
+
+test_that('evaluate_check_ancestry fails with some missing sample error',{
+    expect_error(evaluate_check_ancestry(
+        qcdir, name, prefixMergedDataset="data.HapMapIII_some_samples",
+        refSamples=refSamples),
+        "Not all")
+})
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index c5178eb..b537689 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -41,31 +41,27 @@ df_other$values <- 0.6
 test_that('relatednessFilter throws missing relatedness IID1 column error',{
     expect_error(relatednessFilter(df,relatednessIID1="IID1",
                                    relatednessIID2="ID2",
-                                   relatednessRelatedness="values"),
+                                   relatednessRelatedness="values",
+                                   relatednessTh = 0.185),
                  "Column IID1 for relatedness not found")
 })
 
 test_that('relatednessFilter throws missing relatedness IID2 column error',{
     expect_error(relatednessFilter(df,relatednessIID1="ID1",
                                    relatednessIID2="IID2",
-                                   relatednessRelatedness="values"),
+                                   relatednessRelatedness="values",
+                                   relatednessTh = 0.185),
                  "Column ID1 for relatedness not found")
 })
 
-test_that('relatednessFilter throws missing relatednessTh error',{
-    expect_error(relatednessFilter(df,relatednessIID1="ID1",
-                                   relatednessIID2="ID2",
-                                   relatednessRelatedness="values"),
-                 "argument \"relatednessTh\" is missing, with no default")
-})
-
 
 test_that('relatednessFilter throws missing relatedness FID1 column error',{
     expect_error(relatednessFilter(df,relatednessIID1="ID1",
                                    relatednessIID2="ID2",
                                    relatednessFID1="FID1",
                                    relatednessFID2="FID2",
-                                   relatednessRelatedness="values"),
+                                   relatednessRelatedness="values",
+                                   relatednessTh = 0.185),
                  "Column FID1 for relatedness not found")
 })
 
@@ -95,7 +91,8 @@ test_that('relatednessFilter throws colname specification error',{
     expect_error(relatednessFilter(df, relatednessFID1="FID",
                                    relatednessIID1="ID1",
                                    relatednessIID2="ID2",
-                                   relatednessRelatedness="values"),
+                                   relatednessRelatedness="values",
+                                   relatednessTh = 0.1875),
                  "Either none or both, relatednessFID1 and relatednessFID2")
 })
 
diff --git a/vignettes/AncestryCheck.Rmd b/vignettes/AncestryCheck.Rmd
index 9add4ee..f8f0763 100644
--- a/vignettes/AncestryCheck.Rmd
+++ b/vignettes/AncestryCheck.Rmd
@@ -72,6 +72,36 @@ matching by chromosome, position and alleles. The following sections show how
 to extract the relevant data from the reference and study dataset and how to
 filter matching variants.
 
+### Filter reference and study data for non A-T or G-C SNPs
+We will use an awk script to find A→T and C→G SNPs. As these SNPs are more
+difficult to align and only a subset of SNPs is required for the anlysis, we
+will remove them from both the reference and study data set.
+
+```{bash filter at and gc snps, eval=FALSE}
+awk 'BEGIN {OFS="\t"}  ($5$6 == "GC" || $5$6 == "CG" \
+                        || $5$6 == "AT" || $5$6 == "TA")  {print $2}' \
+    $qcdir/$name.bim  > \
+    $qcdir/$name.ac_gt_snps
+
+awk 'BEGIN {OFS="\t"}  ($5$6 == "GC" || $5$6 == "CG" \
+                        || $5$6 == "AT" || $5$6 == "TA")  {print $2}' \
+    $refdir/$refname.bim  > \
+    $qcdir/$refname.ac_gt_snps
+   
+plink --bfile  $refdir/$refname \
+      --exclude $qcdir/$refname.ac_gt_snps \
+      --make-bed \
+      --out $qcdir/$refname.no_ac_gt_snps
+mv  $qcdir/$refname.no_ac_gt_snps.log $qcdir/plink_log/$refname.no_ac_gt_snps.log
+
+plink --bfile  $qcdir/$name \
+      --exclude $qcdir/$name.ac_gt_snps \
+      --make-bed \
+      --out $qcdir/$name.no_ac_gt_snps
+mv  $qcdir/$name.no_ac_gt_snps.log $qcdir/plink_log/$name.no_ac_gt_snps.log
+```
+
+
 ### Prune study data
 We will conduct principle component analysis on genetic variants that are
 pruned for variants in linkage disequlibrium (LD) with an $r^2 >0.2$ in a 50kb
@@ -82,17 +112,17 @@ ranges of known high-LD structure. This file was originally provided by
 `file.path(find.package('plinkQC'),'extdata','high-LD-regions.txt')`.
 
 ```{bash prune, eval=FALSE}
-plink --bfile  $qcdir/$name \
+plink --bfile  $qcdir/$name.no_ac_gt_snps \
       --exclude range  $refdir/$highld \
       --indep-pairwise 50 5 0.2 \
-      --out $qcdir/$name
-mv  $qcdir/$name.prune.log $qcdir/plink_log/$name.prune
+      --out $qcdir/$name.no_ac_gt_snps
+mv  $qcdir/$name.prune.log $qcdir/plink_log/$name.prune.log
 
-plink --bfile  $qcdir/$name \
-      --extract $qcdir/$name.prune.in \
+plink --bfile  $qcdir/$name.no_ac_gt_snps \
+      --extract $qcdir/$name.no_ac_gt_snps.prune.in \
       --make-bed \
       --out $qcdir/$name.pruned
-mv  $qcdir/$name.pruned.log $qcdir/plink_log/$name.pruned
+mv  $qcdir/$name.pruned.log $qcdir/plink_log/$name.pruned.log
 ```
 
 ### Filter reference data for the same SNP set as in study
@@ -103,7 +133,7 @@ plink --bfile  $refdir/$refname \
       --extract $qcdir/$name.prune.in \
       --make-bed \
       --out $qcdir/$refname.pruned
-mv  $qcdir/$refname.pruned.log $qcdir/plink_log/$refname.pruned
+mv  $qcdir/$refname.pruned.log $qcdir/plink_log/$refname.pruned.log
 ```
 
 ### Check and correct chromosome mismatch
diff --git a/vignettes/Genomes1000.Rmd b/vignettes/Genomes1000.Rmd
index 19db9a4..46022f0 100644
--- a/vignettes/Genomes1000.Rmd
+++ b/vignettes/Genomes1000.Rmd
@@ -64,13 +64,13 @@ corresponds to v1.9, whereas `plink2` corresponds to v2.
 1000 Genomes phase III (1000GenomesIII) is available in
 [PLINK 2 binary format](https://www.cog-genomics.org/plink/2.0/input#pgen) at https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3.
 In addition, a sample file with information about the individuals' ancestry
-is available and shoud be downloaded as in input for `plinkQC::chec_Ancestry()`.
+is available and shoud be downloaded as in input for `plinkQC::check_ancestry()`.
 The following code chunk downloads and decompresses the data.
 The genome build of
 these files is the same as the original release of the 1000GenomesIII, namely
 CGRCh37. 
 
-NB: CGRCh38 positions in vcf format can be found [here](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/)
+NB: CGRCh38 positions in vcf format can be found [here](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/).
 The remainder of this vignette will however look at the data processing required
 for the 1000GenomesIII available in
 [PLINK 2 binary format](https://www.cog-genomics.org/plink/2.0/input#pgen).
diff --git a/vignettes/plinkQC.Rmd b/vignettes/plinkQC.Rmd
index 704e951..a0e59e5 100644
--- a/vignettes/plinkQC.Rmd
+++ b/vignettes/plinkQC.Rmd
@@ -134,8 +134,7 @@ the `qcdir` will often be the same as the `indir` and this step will not be
 required.
 
 ```{r copy files}
-system(paste("cp", file.path(package.dir, 'extdata/data.HapMapIII.eigenvec'),
-             qcdir))
+file.copy(file.path(package.dir, 'extdata/data.HapMapIII.eigenvec'), qcdir)
 ```
 
 `perIndividualQC` displays the results of the quality control steps in a