version 0.5.3

cran · Apr 21, 2020 · 2d2349a · 2d2349a
1 parent 54a711f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: DEploid
 Type: Package
 Title: Deconvolute Mixed Genomes with Unknown Proportions
-Version: 0.5.2
+Version: 0.5.3
 Authors@R: c(
-    person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="joe.zhu@bdi.ox.ac.uk"),
+    person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="sha.joe.zhu@gmail.com"),
     person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
     person('Gil', 'McVean', role=c('aut', 'cph')),
     person('University of Oxford', '', role=c('cph')),
@@ -22,8 +22,8 @@ Description: Traditional phasing programs are limited to diploid organisms.
  patient blood sample, which often contains more than one parasite strain, with
  unknown proportions. This package is used for deconvoluting mixed haplotypes,
  and reporting the mixture proportions from each sample.
-URL: https://github.com/mcveanlab/DEploid-r
-BugReports: https://github.com/mcveanlab/DEploid-r/issues
+URL: https://github.com/DEploid-dev/DEploid-r
+BugReports: https://github.com/DEploid-dev/DEploid-r/issues
 License: GPL (>= 3)
 Depends: R (>= 3.1.0)
 Imports: Rcpp (>= 0.11.2), scales (>= 0.4.0), plotly (>= 4.7.1),
@@ -32,10 +32,10 @@ Suggests: knitr, testthat (>= 0.9.0)
 SystemRequirements: C++11
 VignetteBuilder: knitr
 LinkingTo: Rcpp
-RoxygenNote: 6.0.1
-Date: 2018-10-23
+RoxygenNote: 7.1.0
+Date: 2020-04-21
 NeedsCompilation: yes
-Packaged: 2018-10-23 13:59:50 UTC; joezhu
+Packaged: 2020-04-21 19:54:46 UTC; joezhu
 Author: Joe Zhu [aut, cre, cph],
   Jacob Almagro-Garcia [aut, cph],
   Gil McVean [aut, cph],
@@ -44,6 +44,6 @@ Author: Joe Zhu [aut, cre, cph],
   CodeCogs Zyba Ltd [com, cph],
   Deepak Bandyopadhyay [com, cph],
   Lutz Kettner [com, cph]
-Maintainer: Joe Zhu <joe.zhu@bdi.ox.ac.uk>
+Maintainer: Joe Zhu <sha.joe.zhu@gmail.com>
 Repository: CRAN
-Date/Publication: 2018-10-23 16:50:07 UTC
+Date/Publication: 2020-04-21 22:20:03 UTC
diff --git a/MD5 b/MD5
@@ -1,15 +1,15 @@
-e8832ec23b928272e25a5f5508391e25 *DESCRIPTION
-620dec5abe35747430a215d8d65731bb *NAMESPACE
-3f730ab29544fc1d63946a50242f3a42 *R/DEploidR.R
-7efdf7afe8931c93c9c3cdf32a85fb6b *R/RcppExports.R
-856a9b3317faac53312a512e049ca0f9 *R/dEploid.R
-d3fac2cb88aea885efd78a57cd3b8a06 *R/dEploidPlotly.R
-86e0f5d855f8f024f1be4513711c735d *README.md
-3d5ac8ca720160834e8b1aeedfa70f91 *build/vignette.rds
+47dd0865373a1b4fbc52eaf90845f93d *DESCRIPTION
+a9f200014bea50967b792f8dec0b5deb *NAMESPACE
+3e840db6bd1e7d28e6f883eb7e3d2bf2 *R/DEploidR.R
+bc37f4573416acabe3a5073b9f75cbf9 *R/RcppExports.R
+1735f4b15d2dae88b0a92be746f203e2 *R/dEploid.R
+c120d3b9f5054e36a1eff699a72e65fd *R/dEploidPlotly.R
+c9d4100fd7ad1bb16383c2e12b1f4cea *README.md
+6e48ee515ac69b3ae16322675857c9a9 *build/vignette.rds
 461e2dc267742100128d50cd74e757e2 *inst/CITATION
 01c90976b229646ca9b46399709688e3 *inst/doc/dEploid-Arguments.R
-2cbf6a6a60e07984981e6a2329578f8e *inst/doc/dEploid-Arguments.Rmd
-09e7d0e800948d08935603b27f5e742d *inst/doc/dEploid-Arguments.html
+f6cd38b30fbca1830582f02601a54165 *inst/doc/dEploid-Arguments.Rmd
+2d6a21c8934b4998746528673efc364c *inst/doc/dEploid-Arguments.html
 2cad08193815864d8a26f8ac768ef199 *inst/extdata/PG0390-C.test.alt
 07eccfaeb952de9e0460bcc12d457b22 *inst/extdata/PG0390-C.test.ref
 cdc601c1d8d4eec2bc80512eb8ee6b6b *inst/extdata/PG0390-C.test.vcf.gz
@@ -23,16 +23,19 @@ a7dec0cf819f7b734569760e93f0a0df *man/dEploid.Rd
 d5231f506efc96d0257c95faf60f4c1a *man/extractCoverageFromTxt.Rd
 54c88b77f9b79b1402d0d5b932416e90 *man/extractCoverageFromVcf.Rd
 3b94e99a025a308b8e6df581b33125b6 *man/extractPLAF.Rd
-1d929973d73c6742bd223e1ffc07b15c *man/haplotypePainter.Rd
-d27b68362961277a9dae5718e025b2ee *man/histWSAF.Rd
-c15c6c7d70701d6d454e46553ec8f3fb *man/plotAltVsRef.Rd
+64bca01253dc1d96ad88606e4af1007b *man/extractVcf.Rd
+90ec3a7f0a1c09b7859391a073b063a1 *man/haplotypePainter.Rd
+56b53ff8f140b8fad882a7405e156413 *man/histWSAF.Rd
+8e24181fd012cce857cb89659bc496b4 *man/plotAltVsRef.Rd
 4a719f9ddd20b1604d7ac33f64c9c251 *man/plotAltVsRefPlotly.Rd
 2e3ce3260c47e734c3d0aa28cd153abf *man/plotHistWSAFPlotly.Rd
-aa2e2c6ae4087fd61777c9fa17742152 *man/plotObsExpWSAF.Rd
+7939b97259f91d8bf94d58435a2c2dea *man/plotObsExpWSAF.Rd
 ab1b443b0af8bf81d85e063f3556e80f *man/plotObsExpWSAFPlotly.Rd
-8f91e514e27c39a978351e2a9976ddc6 *man/plotProportions.Rd
-499310d8b94430a9ff1172326bf9f3d5 *man/plotWSAFVsPLAFPlotly.Rd
-57351dea18413509031f78bd2b106dae *man/plotWSAFvsPLAF.Rd
+f022a17d3aba800ec29c8bc84f604a47 *man/plotProportions.Rd
+896f6c0918ae703f90946a82ccc23dbc *man/plotWSAFVsPLAFPlotly.Rd
+b3a1e2e14fde6c8331b95ddad3253a31 *man/plotWSAFvsPLAF.Rd
+84e19633e468db778b959bee6bde90a4 *src/DEploid/chooseK.cpp
+3161cb5ed21dc853ed2c5e0f121fb4e4 *src/DEploid/chooseK.hpp
 c3adb6d6823db1b19840143fa58ba349 *src/DEploid/codeCogs/asympt_expn.h
 9c4cc52f7742819084a453fef38e0288 *src/DEploid/codeCogs/errorfn.h
 09168cd629e28c9591a8b7a276acc1e4 *src/DEploid/codeCogs/errorfnc.h
@@ -50,60 +53,69 @@ ccec2bc4b1d1436416711e52b16ef3e0 *src/DEploid/codeCogs/mersenne.hpp
 3ba8122e26b392c415edec3c7b3ac888 *src/DEploid/codeCogs/randomSample.hpp
 94c33b48dee38eb7bdc87638e718e09e *src/DEploid/codeCogs/stirling.h
 a3585d8d0b267c7076cc835be837bf5f *src/DEploid/codeCogs/xsub_ln_add1.h
-b822188831563922209c5cc0d82499d6 *src/DEploid/dEploidIO.cpp
-71263fc8d2ef0b0c38e6ddaf0d340b34 *src/DEploid/dEploidIO.hpp
+7a9f6dc0d23cdea99d476a04bfba2649 *src/DEploid/dEploidIO.cpp
+a2d485a3483b582a246583cf190ad4d6 *src/DEploid/dEploidIO.hpp
 47c3ccc7c67427b403bf67412c19825c *src/DEploid/debug/mcmcDebug.cpp
 f2bc5a44cdf66b26c3657897be89c337 *src/DEploid/debug/vcfReaderDebug.cpp
 2ab6797644a0dd90391e0dfa38ac9a33 *src/DEploid/exceptions.hpp
-aa0d0dbab21a8daecaf3a90cc3986f65 *src/DEploid/export/dEploidIOExport.cpp
-391762551ff34224643d84913249c130 *src/DEploid/export/dEploidIOExportPosteriorProb.cpp
-8511cebf54bf4ab7ca4b0835b8a06104 *src/DEploid/export/writeMcmcRelated.cpp
-0014dc9c1f11529ce9aff9e4d87b9b9d *src/DEploid/global.hpp
+b5278316bade962a54f8d24dad9f0497 *src/DEploid/export/dEploidIOExport.cpp
+77d1c185ac7c32ebeb53a752a7eade23 *src/DEploid/export/dEploidIOExportPosteriorProb.cpp
+5ad831f40f72baa65459a5a30c9c265d *src/DEploid/export/writeMcmcRelated.cpp
+2bfa262ffc355802a21f5c435c9124a2 *src/DEploid/global.hpp
 7fbc338309ac38fefcd64b04bb903e34 *src/DEploid/gzstream/COPYING.LIB
 d632447d46c9b1d6ab0103de7a665034 *src/DEploid/gzstream/README
 ba512bdbb2404b95b4303f226f9d8ef8 *src/DEploid/gzstream/gzstream.cpp
-99d59b3af2c3974f943e118556645888 *src/DEploid/gzstream/gzstream.h
+4f963f87cdf001ff7525c79019f0ea96 *src/DEploid/gzstream/gzstream.h
 caa5ea78d04f32a480fa6d4008817cec *src/DEploid/gzstream/index.html
 78e2cca98f5d11a43af84eccdd9fb96e *src/DEploid/gzstream/logo.gif
 72767782fc756a7855f92361e949b499 *src/DEploid/gzstream/test_gunzip.C
 ade409024dc2511702be4b25cec98304 *src/DEploid/gzstream/test_gzip.C
-bbd0b64c69d158664fc7f806df5b85b2 *src/DEploid/ibd.cpp
-0d527d3a676ae668cebc41b55bfd810e *src/DEploid/ibd.hpp
+a2f7507870a6d0a9c857cbdf814b77c2 *src/DEploid/ibd.cpp
+e6a7d41b98a99f5d0937cea7b397e90f *src/DEploid/ibd.hpp
 be3900f55cf510e4011fc09aebbd469e *src/DEploid/lasso/dEploidLasso.cpp
 70b70d4a42bfa2673e799f8eb6697576 *src/DEploid/lasso/dEploidLasso.hpp
 8d7d21d3dbfd7eeda6783eeb172dc00d *src/DEploid/lasso/dbgmacro.hpp
 b1243a1e6ca579543c49bc30cfd79dce *src/DEploid/lasso/lasso.cpp
 e77974455e21e3fbc36f3d66a1464cc3 *src/DEploid/lasso/lasso.hpp
 a60b6085198e7396d5392472e7d8f3ad *src/DEploid/lasso/lassoDBG.cpp
-196cfe16ca992fb0e11539bed7372329 *src/DEploid/mcmc.cpp
-c8a50d58b170f744e3e764446bf2512b *src/DEploid/mcmc.hpp
-94a7d14022d6977963a596d991cf49cc *src/DEploid/panel.cpp
-738a29be3df64f963520a408ba5ab91a *src/DEploid/panel.hpp
+25838ce7135152cc75c3f07910eb49da *src/DEploid/lasso/src/dEploidLasso.cpp
+70b70d4a42bfa2673e799f8eb6697576 *src/DEploid/lasso/src/dEploidLasso.hpp
+8d7d21d3dbfd7eeda6783eeb172dc00d *src/DEploid/lasso/src/dbgmacro.hpp
+03b4b4ed9f59e5b323be6709dee187dc *src/DEploid/lasso/src/lasso.cpp
+46061222bfd5d5fdc6c013b5bcf6a527 *src/DEploid/lasso/src/lasso.hpp
+a60b6085198e7396d5392472e7d8f3ad *src/DEploid/lasso/src/lassoDBG.cpp
+84dcf4a918f976f8a6fa59e2de905949 *src/DEploid/lasso/src/lassoOut.cpp
+806cb8d3c8f627198ebfb306d2d19a4e *src/DEploid/lasso/src/main.cpp
+8dc446c85ea8f09937b1b44b501bcd01 *src/DEploid/mcmc.cpp
+b1f3be122f6b92974cf7f6d0e1f90c5a *src/DEploid/mcmc.hpp
+9a113321923c7722d06dea76c943768d *src/DEploid/panel.cpp
+89e3bb9bee61958000bdd05113ddc9dd *src/DEploid/panel.hpp
 a6765fb4db45924b1d3b2d7ed6d5b0ae *src/DEploid/random/fastfunc.cpp
 1a598d9c9df966427a64ef6a74ce56d5 *src/DEploid/random/fastfunc.hpp
 d7ee5456f67c91bd7da907001965dd72 *src/DEploid/random/mersenne_twister.cpp
 5c40c783d72b75abcd7a5264a74d4c1a *src/DEploid/random/mersenne_twister.hpp
 9563d50543ff7687795b66906c787a9f *src/DEploid/random/random_generator.cpp
 ad21a81bdcb9369d4c7f9b2d54cb37be *src/DEploid/random/random_generator.hpp
-7e510de097c6a4b82343f8dbaba4cabe *src/DEploid/txtReader.cpp
-9e33ed23ec1e99b143de552cb4c47f08 *src/DEploid/txtReader.hpp
-8fa54dd0674c17dd90c0f99607b3640f *src/DEploid/updateHap.cpp
+21fb5b8d81f87fece7386042ee93080f *src/DEploid/txtReader.cpp
+d91e32b2cbdb99b7a4de19a1e300bfcc *src/DEploid/txtReader.hpp
+bb5c0c16b193c8d23e6ca749f9caa120 *src/DEploid/updateHap.cpp
 3c04f03a2e9e8c022ff6138ce0f5dd67 *src/DEploid/updateHap.hpp
 177058e9bd41a4d0905b8cc8b6a9fa50 *src/DEploid/utility.cpp
 20acd35532218e8d275c8b1aff30df36 *src/DEploid/utility.hpp
-6befb905c2f2db83e6703cf5de751983 *src/DEploid/variantIndex.cpp
-1a0ca7691a0ad14a2f03b23511337fc7 *src/DEploid/variantIndex.hpp
-87165591ce55df9e0352b0833d5fd14a *src/DEploid/vcfReader.cpp
-35b5749b31bae39d02661b505450f46c *src/DEploid/vcfReader.hpp
-c4002d59b81406e8bc6fe9eb5535e2c7 *src/Makevars
-c4002d59b81406e8bc6fe9eb5535e2c7 *src/Makevars.win
-2b97b24c7193853b75825b3fb76daa7e *src/RcppExports.cpp
-d8d7321b0ef6566648a7f7c25b3c775c *src/dEploidr.cpp
-c5cc16e00e5cd1b8150a274c1fcfd3ad *src/init.c
+65330fa96e44f48a7b85c73750f0b108 *src/DEploid/variantIndex.cpp
+6d4f3e64f6db7dbecaa70d26eec74aee *src/DEploid/variantIndex.hpp
+4aebd4559607f84d5e7f3e99c022fba2 *src/DEploid/vcfReader.cpp
+09fdba583594f73c14cac4b80a839bdd *src/DEploid/vcfReader.hpp
+c7de0a31de0254cbc5e788991439c126 *src/Makevars
+c7de0a31de0254cbc5e788991439c126 *src/Makevars.win
+9851cbb04beb870628887bd9fd4aea95 *src/RcppExports.cpp
+d8978e86ef248b69b5cbacdf772d9947 *src/dEploidr.cpp
+078261833097c896bbfc76b9ca1d9fc9 *src/init.c
 d9780788cb9e10ae63d0cfb4ce81703d *src/r_random_generator.h
+9d238cfbf5bb3246fdfe3450d0a4783c *src/rvcf.cpp
 eedb9b59a5a966b63e9e82308caf7349 *src/test_exports.cpp
 e095660d571c0f3ef91ce1211ecb7f76 *tests/testthat.R
-9d2d8716411d1971ee55a3faca5fad34 *tests/testthat/test-DEploid_tools.R
-e6096201933e4b6042e165bca5d80db7 *tests/testthat/test-dEploid.R
+2e864ff1e075a03cfb767d0a72847d40 *tests/testthat/test-DEploid_tools.R
+01ca5f935513941e0e097f4bdbf3d02c *tests/testthat/test-dEploid.R
 f66b335af2d854e56592824fc8df7a0a *tests/testthat/test-r_random-generator.R
-2cbf6a6a60e07984981e6a2329578f8e *vignettes/dEploid-Arguments.Rmd
+f6cd38b30fbca1830582f02601a54165 *vignettes/dEploid-Arguments.Rmd
diff --git a/NAMESPACE b/NAMESPACE
@@ -9,6 +9,7 @@ importFrom("rmarkdown", "pandoc_available")
 importFrom("htmlwidgets", "saveWidget")
 useDynLib(DEploid, .registration = TRUE)
 export(dEploid)
+export(extractVcf)
 export(plotProportions)
 export(extractCoverageFromVcf)
 export(extractCoverageFromTxt)

diff --git a/R/DEploidR.R b/R/DEploidR.R
@@ -20,7 +20,8 @@
 #' altFile = system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
 #' PG0390 = extractCoverageFromTxt(refFile, altFile)
 #'
-extractCoverageFromTxt <- function(refFileName, altFileName){
+
+extractCoverageFromTxt <- function(refFileName, altFileName) {
     ref <- read.table(refFileName, header = TRUE, comment.char = "")
     alt <- read.table(altFileName, header = TRUE, comment.char = "")
     return(data.frame(CHROM = ref[, 1],
@@ -51,18 +52,19 @@ extractCoverageFromTxt <- function(refFileName, altFileName){
 #' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
 #' PG0390 = extractCoverageFromVcf(vcfFile)
 #'
-extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
+
+extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2) {
     # Assume that AD is the second field
-    h <- function(w){
+    h <- function(w) {
          if (any(grepl("gzfile connection", w)))
          invokeRestart("muffleWarning")
     }
 
     gzf <- gzfile(vcfFileName, open = "rb")
     numberOfHeaderLines <- 0
     line <- withCallingHandlers(readLines(gzf, n = 1), warning = h)
-    while (length(line) > 0){
-        if (grepl("##", line)){
+    while (length(line) > 0) {
+        if (grepl("##", line)) {
             numberOfHeaderLines <- numberOfHeaderLines + 1
         } else {
             break
@@ -111,7 +113,8 @@ extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
 #'   package = "DEploid")
 #' plaf = extractPLAF(plafFile)
 #'
-extractPLAF <- function(plafFileName){
+
+extractPLAF <- function(plafFileName) {
     return(read.table(plafFileName, header = T)$PLAF)
 }
 
@@ -148,8 +151,9 @@ extractPLAF <- function(plafFileName){
 #' plotProportions(PG0390Coverage.deconv$Proportions, "PG0390-C proportions")
 #' }
 #'
+
 plotProportions <- function(proportions, title = "Components",
-                       cex.lab = 1, cex.main = 1, cex.axis = 1){
+                       cex.lab = 1, cex.main = 1, cex.axis = 1) {
     rainbowColorBin <- 16
     barplot(t(proportions), beside = F, border = NA,
         col = rainbow(rainbowColorBin), space = 0, xlab = "Iteration",
@@ -197,10 +201,11 @@ plotProportions <- function(proportions, title = "Components",
 #' PG0390CoverageV = extractCoverageFromVcf(vcfFile)
 #' plotAltVsRef(PG0390CoverageV$refCount, PG0390CoverageV$altCount)
 #'
+
 plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
                     exclude.ref = c(), exclude.alt = c(),
                     potentialOutliers = c(), cex.lab = 1, cex.main = 1,
-                    cex.axis = 1){
+                    cex.axis = 1) {
     cr <- colorRampPalette(colors = c("#de2d26", "#2b8cbe"))
     colors <- cr(31)
     ratios <- ref / (ref + alt + 0.0000001)
@@ -220,7 +225,7 @@ plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
     abline(h = 150, untf = FALSE, lty = 2)
     abline(v = 150, untf = FALSE, lty = 2)
 
-    if (length(potentialOutliers) > 0){
+    if (length(potentialOutliers) > 0) {
         points(ref[potentialOutliers], alt[potentialOutliers], col = "black",
                pch = "x", cex = 2)
     }
@@ -265,10 +270,10 @@ plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
 #'
 histWSAF <- function(obsWSAF, exclusive = TRUE,
                 title ="Histogram 0<WSAF<1",
-                cex.lab = 1, cex.main = 1, cex.axis = 1){
-    tmpWSAFIndex <- 1:length(obsWSAF)
-    if (exclusive){
-        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
+                cex.lab = 1, cex.main = 1, cex.axis = 1) {
+    tmpWSAFIndex <- seq_len(length(obsWSAF))
+    if (exclusive) {
+        tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
     }
     return(hist(obsWSAF[tmpWSAFIndex], main = title,
         breaks = seq(0, 1, by = 0.1), xlab = "WSAF", col = "gray",
@@ -322,14 +327,14 @@ histWSAF <- function(obsWSAF, exclusive = TRUE,
 #'
 plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                       potentialOutliers = c(), title = "WSAF vs PLAF",
-                      cex.lab = 1, cex.main = 1, cex.axis = 1){
+                      cex.lab = 1, cex.main = 1, cex.axis = 1) {
     plot(plaf, obsWSAF, cex = 0.5, xlim = c(0, 1), ylim = c(0, 1),
         col = "red", main = title, xlab = "PLAF", ylab = "WSAF",
         cex.lab = cex.lab, cex.main = cex.main, cex.axis = cex.axis)
-    if (length(expWSAF) > 0){
+    if (length(expWSAF) > 0) {
         points(plaf, expWSAF, cex = 0.5, col = "blue")
     }
-    if (length(potentialOutliers) > 0){
+    if (length(potentialOutliers) > 0) {
         points(plaf[potentialOutliers], obsWSAF[potentialOutliers],
         col = "black", pch = "x", cex = 2)
     }
@@ -363,16 +368,16 @@ plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
 #' obsWSAF = computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
 #' plafFile = system.file("extdata", "labStrains.test.PLAF.txt",
 #'  package = "DEploid")
-#' PG0390CoverageV.deconv = dEploid(paste("-vcf", vcfFile,
+#' PG0390.deconv = dEploid(paste("-vcf", vcfFile,
 #'                                        "-plaf", plafFile, "-noPanel"))
-#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
-#' expWSAF = t(PG0390CoverageV.deconv$Haps) %*% prop
+#' prop = PG0390.deconv$Proportions[dim(PG0390.deconv$Proportions)[1],]
+#' expWSAF = t(PG0390.deconv$Haps) %*% prop
 #' plotObsExpWSAF(obsWSAF, expWSAF)
 #' }
 #'
 plotObsExpWSAF <- function(obsWSAF, expWSAF,
                       title = "WSAF(observed vs expected)",
-                      cex.lab = 1, cex.main = 1, cex.axis = 1){
+                      cex.lab = 1, cex.main = 1, cex.axis = 1) {
     plot(obsWSAF, expWSAF, pch = 19, col = "blue",
         xlab = "Observed WSAF (ALT/(ALT+REF))", ylab = "Expected WSAF (h%*%p)",
         main = title, xlim = c(-0.05, 1.05), cex = 0.5, ylim = c(-0.05, 1.05),
@@ -408,7 +413,7 @@ plotObsExpWSAF <- function(obsWSAF, expWSAF,
 #' PG0390CoverageV = extractCoverageFromVcf(vcfFile)
 #' obsWSAF = computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
 #'
-computeObsWSAF <- function(alt, ref){
+computeObsWSAF <- function(alt, ref) {
     return(alt / (ref + alt + 0.00000001))
 }
 
@@ -430,10 +435,10 @@ computeObsWSAF <- function(alt, ref){
 #' @export
 #'
 haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
-                        numberOfInbreeding = 0){
+                        numberOfInbreeding = 0) {
     rainbowColorBin <- 16
     rainbowColors <- rainbow(rainbowColorBin)
-    if (numberOfInbreeding > 0){
+    if (numberOfInbreeding > 0) {
         panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
         rainbowColors <- c(rep("#46a8e1", panelSize),
                            rep("#f34747", numberOfInbreeding))

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -40,6 +40,36 @@ dEploid <- function(args) {
     .Call(`_DEploid_dEploid`, args)
 }
 
+#' @title Extract VCF information
+#'
+#' @description Extract VCF information
+#'
+#' @param filename VCF file name.
+#'
+#' @seealso
+#' \itemize{
+#'   \item \code{extractCoverageFromVcf}
+#'   \item \code{extractCoverageFromTxt}
+#' }
+#'
+#' @return A dataframe list with members of haplotypes, proportions and log likelihood of the MCMC chain.
+#' \itemize{
+#'   \item \code{CHROM} SNP chromosomes.
+#'   \item \code{POS} SNP positions.
+#'   \item \code{refCount} reference allele count.
+#'   \item \code{altCount} alternative allele count.
+#' }
+#'
+#' @export
+#'
+#' @examples
+#' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' vcf = extractVcf(vcfFile)
+#'
+extractVcf <- function(filename) {
+    .Call(`_DEploid_extractVcf`, filename)
+}
+
 test_RRG_sample <- function() {
     .Call(`_DEploid_test_RRG_sample`)
 }