Zipped more example files to reduce package size.

ddrichel · Feb 26, 2022 · 4a7f481 · 4a7f481
1 parent da76569
commit 4a7f481
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Showing 39 changed files with 103 additions and 40,303 deletions.
diff --git a/R/annotateTargets.R b/R/annotateTargets.R
@@ -16,9 +16,9 @@
 #' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
 #' library(org.Hs.eg.db)
 #'
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt",
-#'     package="PureCN")
-#' x <- head(readCoverageFile(normal.coverage.file),100)
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",
+#'     package = "PureCN")
+#' x <- head(readCoverageFile(normal.coverage.file), 100)
 #' x <- annotateTargets(x,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db)
 #'
 #' @importFrom GenomicFeatures transcriptsByOverlaps exonsByOverlaps cdsByOverlaps

diff --git a/R/calculateLogRatio.R b/R/calculateLogRatio.R
@@ -15,10 +15,10 @@
 #' @author Markus Riester
 #' @examples
 #' 
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt", 
-#'     package="PureCN")
-#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt", 
-#'     package="PureCN")
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz", 
+#'     package = "PureCN")
+#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz", 
+#'     package = "PureCN")
 #' normal <- readCoverageFile(normal.coverage.file)
 #' tumor <- readCoverageFile(tumor.coverage.file)
 #' log.ratio <- calculateLogRatio(normal, tumor)

diff --git a/R/callAmplificationsInLowPurity.R b/R/callAmplificationsInLowPurity.R
@@ -27,10 +27,10 @@
 #' @examples
 #' 
 #' data(purecn.example.output)
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt", 
-#'     package="PureCN")
-#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt", 
-#'     package="PureCN")
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz", 
+#'     package = "PureCN")
+#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz", 
+#'     package = "PureCN")
 #' normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
 #' normalDB <- createNormalDatabase(normal.coverage.files)
 #' callAmplificationsInLowPurity(purecn.example.output, normalDB)["EIF2A", ]

diff --git a/R/correctCoverageBias.R b/R/correctCoverageBias.R
@@ -29,7 +29,7 @@ globalVariables(names = c("..level.."))
 #' @seealso \code{\link{preprocessIntervals}}
 #' @examples
 #'
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt",
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",
 #'     package = "PureCN")
 #' interval.file <- system.file("extdata", "example_intervals.txt",
 #'     package = "PureCN")

diff --git a/R/createNormalDatabase.R b/R/createNormalDatabase.R
@@ -29,9 +29,9 @@
 #' @seealso \code{\link{calculateTangentNormal}}
 #' @examples
 #'
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt",
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",
 #'     package = "PureCN")
-#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
+#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",
 #'     package = "PureCN")
 #' normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
 #' normalDB <- createNormalDatabase(normal.coverage.files)
@@ -281,12 +281,12 @@ optimal.off.target.counts = 120, plot = FALSE, ...) {
 #' @author Markus Riester
 #' @examples
 #'
-#' tumor.coverage.file <- system.file('extdata', 'example_tumor.txt', 
-#'     package='PureCN')
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt", 
-#'     package="PureCN")
-#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt", 
-#'     package="PureCN")
+#' tumor.coverage.file <- system.file('extdata', 'example_tumor.txt.gz', 
+#'     package = 'PureCN')
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz", 
+#'     package = "PureCN")
+#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz", 
+#'     package = "PureCN")
 #' normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
 #' normalDB <- createNormalDatabase(normal.coverage.files)
 #' pool <- calculateTangentNormal(tumor.coverage.file, normalDB)

diff --git a/R/filterIntervals.R b/R/filterIntervals.R
@@ -36,14 +36,14 @@
 #' @author Markus Riester
 #' @examples
 #'
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt",
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",
 #'     package = "PureCN")
-#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
+#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",
 #'     package = "PureCN")
 #' normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
 #' normalDB <- createNormalDatabase(normal.coverage.files)
 #'
-#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt",
+#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz",
 #'     package = "PureCN")
 #' vcf.file <- system.file("extdata", "example.vcf.gz",
 #'     package = "PureCN")

diff --git a/R/getSex.R b/R/getSex.R
@@ -25,7 +25,7 @@
 #' @seealso \code{\link{getSexFromVcf}}
 #' @examples
 #'
-#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt",
+#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz",
 #'     package = "PureCN")
 #' sex <- getSexFromCoverage(tumor.coverage.file)
 #'

diff --git a/R/poolCoverage.R b/R/poolCoverage.R
@@ -12,9 +12,9 @@
 #' @seealso \code{\link{readCoverageFile}}
 #' @examples
 #'
-#' normal.coverage.file <- system.file("extdata", "example_normal.txt",
+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",
 #'     package = "PureCN")
-#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
+#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",
 #'     package = "PureCN")
 #' normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
 #' pool <- poolCoverage(lapply(normal.coverage.files, readCoverageFile),

diff --git a/R/processMultipleSamples.R b/R/processMultipleSamples.R
@@ -33,13 +33,13 @@
 #' @seealso \code{\link{runAbsoluteCN}}
 #' @examples
 #'
-#' normal1.coverage.file <- system.file("extdata", "example_normal.txt",
+#' normal1.coverage.file <- system.file("extdata", "example_normal.txt.gz",
 #'     package = "PureCN")
-#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
+#' normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",
 #'     package = "PureCN")
-#' tumor1.coverage.file <- system.file("extdata", "example_tumor.txt",
+#' tumor1.coverage.file <- system.file("extdata", "example_tumor.txt.gz",
 #'     package = "PureCN")
-#' tumor2.coverage.file <- system.file("extdata", "example_tumor2.txt",
+#' tumor2.coverage.file <- system.file("extdata", "example_tumor2.txt.gz",
 #'     package = "PureCN")
 #'
 #' normal.coverage.files <- c(normal1.coverage.file, normal2.coverage.file)

diff --git a/R/readCoverageFile.R b/R/readCoverageFile.R
@@ -16,15 +16,15 @@
 #' @seealso \code{\link{calculateBamCoverageByInterval}}
 #' @examples
 #' 
-#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt", 
-#'     package="PureCN")
+#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz", 
+#'     package = "PureCN")
 #' coverage <- readCoverageFile(tumor.coverage.file)
-#' 
+#'
 #' @importFrom tools file_ext
 #' @importFrom rhdf5 H5Fopen
 #' @importFrom data.table fread
 #' @export readCoverageFile
-readCoverageFile <- function(file, format, zero=NULL, read.length = 100) {
+readCoverageFile <- function(file, format, zero = NULL, read.length = 100) {
     if (missing(format)) format <- .getFormat(file)
     if (format %in% c("cnn", "cnr")) {
         targetCoverage <- .readCoverageCnn(file, zero, format)