stringsAsFactors as the culprit, addressing #16

meyer-lab-cshl · Sep 24, 2019 · fc7a38b1f2b345d9c6c5d69f5dcf0bc57a857f62 · fc7a38b
1 parent 02f58ea
commit fc7a38b1f2b345d9c6c5d69f5dcf0bc57a857f62
Unified Split

Showing with 6 additions and 4 deletions.

+2 −2 R/individualQC.R

+4 −2 R/utils.R
diff --git a/R/individualQC.R b/R/individualQC.R
@@ -1652,15 +1652,15 @@ evaluate_check_relatedness <- function(qcdir, name, highIBDTh=0.1875,
     testNumerics(numbers=highIBDTh, positives=highIBDTh, proportions=highIBDTh)
     names_imiss <- c("FID", "IID", "MISS_PHENO", "N_MISS", "N_GENO", "F_MISS")
     imiss <- read.table(paste(prefix, ".imiss", sep=""), header=TRUE,
-                        as.is=TRUE)
+                        as.is=TRUE, stringsAsFactors=FALSE)
     if (!all(names_imiss == names(imiss))) {
         stop("Header of ", prefix, ".imiss is not correct. Was your
              file generated with plink --imiss?")
     }
     names_genome <- c("FID1", "IID1", "FID2", "IID2", "RT", "EZ", "Z0", "Z1",
                       "Z2", "PI_HAT", "PHE", "DST", "PPC", "RATIO")
     genome <- read.table(paste(prefix, ".genome", sep=""), header=TRUE,
-                         as.is=TRUE)
+                         as.is=TRUE, stringsAsFactors=FALSE)
     if (!all(names_genome == names(genome))) {
         stop("Header of ", prefix, ".genome is not correct. Was your
              file generated with plink --genome?")

diff --git a/R/utils.R b/R/utils.R
@@ -411,9 +411,11 @@ relatednessFilter <- function(relatedness, otherCriterion=NULL,
         uniqueFails <- relatednessFails[!duplicated(relatednessFails[,iid1_index]),]
         if (!is.null(relatednessFID2)) {
             failIDs <- data.frame(FID=uniqueFails[,fid1_index],
-                              IID=uniqueFails[,iid1_index])
+                              IID=uniqueFails[,iid1_index],
+                              stringsAsFactors=FALSE)
         } else {
-            failIDs <- data.frame(IID=uniqueFails[,iid1_index])
+            failIDs <- data.frame(IID=uniqueFails[,iid1_index],
+                                  stringsAsFactors=FALSE)
         }
     }
     return(list(relatednessFails=relatednessFails, failIDs=failIDs))