Adding files

CNVMetrics.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

R/CNVMetrics.R

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+#' CNVMetrics: Copy number variant metrics
+#'
+#' This package implements metrics to facilite copy number variant 
+#' comparison among samples and/or methods.
+#'
+#' @docType package
+#'
+#' @name CNVMetrics-package
+#'
+#' @aliases CNVMetrics-package CNVMetrics
+#'
+#' @author Astrid Deschênes and
+#' Pascal Belleau
+#'
+#' Maintainer:
+#' Astrid Deschenes <[email protected]>
+#'
+#' @keywords package
+NULL

R/readFiles.R

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+#' @param filepath a \code{character} string, the path to the file to 
+#' read. Alternatively can be a connection.
+#'
+#' @param uniqueTag a \code{character} string, the unique name assigned to
+#' the segment data associated to this file. Each imported file should
+#' have a unique tag.
+#'
+#' @param header a \code{logical}, when \code{TRUE}, the
+#' file has a header that should not be imported. Default: \code{FALSE}.
+#'
+#' @return a \code{GRanges} containing the segment information from the file.
+#'
+#' @examples
+#'
+#' # TODO
+#' 
+#' @author Astrid Deschenes, Pascal Belleau
+#' @importFrom GenomicRanges GRanges
+#' @export
+readSEGFile <- function(filepath, uniqueTag, header=FALSE) {
+
+    if (!is.character(uniqueTag)) {
+        stop("uniqueTag must be a character string.")
+    }
+
+    if (!is.logical(header)) {
+        stop("header must be a logical value.")
+    }
+
+    data <- read.table(filepath, header=header)
+
+    if (nrow(data) < 6) {
+        stop("The segment file must have at least 6 columns.")
+    }
+
+    dataRanges <- GRanges(seqnames = data$V2, 
+                          ranges=IRanges(start=data$V3, end=data$V4), 
+                          score=data$V6, source=uniqueTag)
+
+    return(dataRanges)
+}

README.md

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+
 # CNVMetrics
-R Package to compare copy number variant (CNV) results from multiple samples
+
+A R package to compare copy number variant (CNV) results from multiple samples/methods.
+
+
+## Authors ##
+
+[Astrid Deschênes](http://ca.linkedin.com/in/astriddeschenes "Astrid Deschênes") and
+[Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau "Pascal Belleau")
+
+
+## License ##
+
+This package and the underlying CNVMetrics code are distributed under 
+the Artistic license 2.0. You are free to use and redistribute this software. 
+
+For more information on Artistic 2.0 License see
+[http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)