update doc

R/all_tools.R

@@ -72,11 +72,11 @@ extractPLAF <- function(plafFileName) {
 #' refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
 #' altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
 #' PG0390CoverageTxt <- extractCoverageFromTxt(refFile, altFile)
-#' #PG0390CoverageTxt.deconv <- dEploid(paste(
+#' # PG0390CoverageTxt.deconv <- dEploid(paste(
 #' #   "-ref", refFile, "-alt", altFile,
 #' #   "-plaf", plafFile, "-noPanel"
-#' #))
-#' #plotProportions(PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions")
+#' # ))
+#' # plotProportions(PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions")
 #'
 plotProportions <- function(proportions, title = "Components",
                             cex.lab = 1, cex.main = 1, cex.axis = 1) {
@@ -189,7 +189,7 @@ plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
 #'
 #' # Example 2
 #' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
-#' PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile)
+#' PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
 #' obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount)
 #' histWSAF(obsWSAF)
 #' myhist <- histWSAF(obsWSAF, FALSE)
@@ -244,7 +244,7 @@ histWSAF <- function(obsWSAF, exclusive = TRUE,
 #'
 #' # Example 2
 #' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
-#' PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile)
+#' PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
 #' obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount)
 #' plafFile <- system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid.utils")
 #' plaf <- extractPLAF(plafFile)
@@ -328,7 +328,7 @@ plotObsExpWSAF <- function(obsWSAF, expWSAF,
 #'
 #' # Example 2
 #' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
-#' PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile)
+#' PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
 #' obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount)
 #'
 computeObsWSAF <- function(alt, ref) {

tests/testthat/test-extractFromVCF.R

@@ -1,4 +1,3 @@
-
 #' @title Extract read counts from VCF
 #'
 #' @description Extract read counts from VCF file of a single sample.
@@ -15,14 +14,15 @@
 #'  allele count, alternative allele count.
 #'
 #' @examples
-#' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
-#' PG0390 = extractCoverageFromVcf(vcfFile)
+#' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' PG0390 <- extractCoverageFromVcf(vcfFile)
 #'
 old_extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2) {
   # Assume that AD is the second field
   h <- function(w) {
-    if (any(grepl("gzfile connection", w)))
+    if (any(grepl("gzfile connection", w))) {
       invokeRestart("muffleWarning")
+    }
   }
 
   gzf <- gzfile(vcfFileName, open = "rb")
@@ -38,9 +38,11 @@ old_extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2) {
   }
   close(gzf)
 
-  vcf <- read.table(gzfile(vcfFileName), skip = numberOfHeaderLines,
-                    header = T, comment.char = "", stringsAsFactors = FALSE,
-                    check.names = FALSE)
+  vcf <- read.table(gzfile(vcfFileName),
+    skip = numberOfHeaderLines,
+    header = T, comment.char = "", stringsAsFactors = FALSE,
+    check.names = FALSE
+  )
 
   sampleName <- names(vcf)[10]
 
@@ -53,22 +55,20 @@ old_extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2) {
   refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
   altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
 
-  return(data.frame(CHROM = vcf[, 1],
-                    POS = vcf[, 2],
-                    refCount = refCount,
-                    altCount = altCount))
+  return(data.frame(
+    CHROM = vcf[, 1],
+    POS = vcf[, 2],
+    refCount = refCount,
+    altCount = altCount
+  ))
 }
 
 
-test_that("test R vs cpp vcf extract",
-          {
-            vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
-            vcf = extractCoverageFromVcf(vcfFile, "PG0390-C")
-            PG0390 = old_extractCoverageFromVcf(vcfFile)
-            testthat::expect_equal(names(vcf), names(PG0390))
-            testthat::expect_equal(vcf$CHROM, PG0390$CHROM)
-            testthat::expect_equal(vcf$POS, PG0390$POS)
-            testthat::expect_equal(vcf$refCount, PG0390$refCount)
-            testthat::expect_equal(vcf$altCount, PG0390$altCount)
-          }
-)
+test_that("test R vs cpp vcf extract", {
+  PG0390 <- old_extractCoverageFromVcf(vcfFileName)
+  testthat::expect_equal(names(PG0390CoverageVcf), names(PG0390))
+  testthat::expect_equal(PG0390CoverageVcf$CHROM, PG0390$CHROM)
+  testthat::expect_equal(PG0390CoverageVcf$POS, PG0390$POS)
+  testthat::expect_equal(PG0390CoverageVcf$refCount, PG0390$refCount)
+  testthat::expect_equal(PG0390CoverageVcf$altCount, PG0390$altCount)
+})

tests/testthat/test-vcfreader.R

@@ -1,16 +1,3 @@
-vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
-                           package = "DEploid.utils")
-plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
-                            package = "DEploid.utils")
-panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
-                             package = "DEploid.utils")
-refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
-altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
-
-PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName, "PG0390-C")
-plaf <- extractPLAF(plafFileName)
-
-
 test_that("Extracted coverage", {
   PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
   expect_that(PG0390CoverageTxt, is_a("data.frame"))
@@ -35,8 +22,10 @@ test_that("computeObsWSAF", {
 
 
 test_that("WSAF Related", {
-  obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
-                            PG0390CoverageVcf$refCount)
+  obsWSAF <- computeObsWSAF(
+    PG0390CoverageVcf$altCount,
+    PG0390CoverageVcf$refCount
+  )
   potentialOutliers <- c(5, 12, 25, 30, 35, 50)
 
   expect_that(histWSAF(obsWSAF), is_a("histogram"))
@@ -53,8 +42,10 @@ test_that("WSAF Related", {
 
 
 test_that("plotAltVsRef", {
-  expect_null(plotAltVsRef(PG0390CoverageVcf$refCount,
-                           PG0390CoverageVcf$altCount))
+  expect_null(plotAltVsRef(
+    PG0390CoverageVcf$refCount,
+    PG0390CoverageVcf$altCount
+  ))
   png("AltVsRef.png")
   plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount)
   dev.off()
@@ -64,11 +55,12 @@ test_that("plotAltVsRef", {
 test_that("plotAltVsRefWithOutliers", {
   potentialOutliers <- c(1, 10, 20, 30, 40)
   expect_null(plotAltVsRef(PG0390CoverageVcf$refCount,
-                           PG0390CoverageVcf$altCount,
-                           potentialOutliers = potentialOutliers))
+    PG0390CoverageVcf$altCount,
+    potentialOutliers = potentialOutliers
+  ))
   png("AltVsRefOutlier.png")
   plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount,
-               potentialOutliers = potentialOutliers)
+    potentialOutliers = potentialOutliers
+  )
   dev.off()
 })
-