[Seqinr-commits] r1566 - pkg/man

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2009-03-11 11:02:26 +0100 (Wed, 11 Mar 2009)
New Revision: 1566

Added:
   pkg/man/readBins.Rd
   pkg/man/readPanels.Rd
Log:
new utility functions

Added: pkg/man/readBins.Rd
===================================================================
--- pkg/man/readBins.Rd	                        (rev 0)
+++ pkg/man/readBins.Rd	2009-03-11 10:02:26 UTC (rev 1566)
@@ -0,0 +1,48 @@
+\name{readBins}
+\alias{readBins}
+\title{Import GenMapper Bins configuration file}
+\description{
+In a Bins configuration file there is a description for a given identification
+kit of the expected allele sizes for all the markers available in the kit.
+}
+\usage{
+readBins(file, 
+  colnames = c("allele.name", "size.bp", "minus.bp", "plus.bp"))}
+\arguments{
+  \item{file}{The name of the Bins configuration file.}
+  \item{colnames}{The names to be used for the columns of the data.frames.}
+}
+\value{
+A list whose first element is the file header info and following elements
+are lists, one for each kit encountered in the file. For each kit we have
+a list of data.frames, one per marker.
+}
+\details{
+The expected allele sizes are typically plus or minus 0.5 bp.
+}
+\references{ 
+\code{citation("seqinR")}
+}
+\author{J.R. Lobry}
+\seealso{\code{\link{readPanels}}.}
+\examples{
+#
+# Check that we can read the 2 exemple files in the seqinR package:
+#
+path1 <- system.file("abif/AmpFLSTR_Bins_v1.txt", package = "seqinr")
+resbin1 <- readBins(path1)
+path2 <- system.file("abif/Promega_Bins_v1.txt", package = "seqinr")
+resbin2 <- readBins(path2)
+#
+# Show the kits described in resbin1:
+#
+names(resbin1)
+#
+# Show the markers in a given kit:
+#
+names(resbin1[["Identifiler_v1"]])
+#
+# Show alleles expected sizes for a given marker:
+#
+resbin1[["Identifiler_v1"]][["D8S1179"]]
+}

Added: pkg/man/readPanels.Rd
===================================================================
--- pkg/man/readPanels.Rd	                        (rev 0)
+++ pkg/man/readPanels.Rd	2009-03-11 10:02:26 UTC (rev 1566)
@@ -0,0 +1,70 @@
+\name{readPanels}
+\alias{readPanels}
+\title{Import GenMapper Panels configuration file}
+\description{
+In a Panel configuration file there is a description for a given identification
+kit of the marker names, their dye label color, expected size range,
+expected positive control genotypes, number of bases in core repeat,
+stutter percentages, and allele names.
+}
+\usage{
+readPanels(file,
+  colnames = c("marker", "dye.col", "min.bp", "max.bp", "exp.pcg", "repeat.bp",
+    "stutter.pc", "uknw", "allele names"))}
+\arguments{
+  \item{file}{The name of the Panel configuration file.}
+  \item{colnames}{The names to be used for the columns of the data.frames.}
+}
+\value{
+A list whose first element is the file header info and following elements
+data.frames, one for each kit encountered in the file.
+}
+\details{
+Number of bases in core repeat is set to 9 for Amelogenin locus.
+}
+\references{ 
+\code{citation("seqinR")}
+}
+\author{J.R. Lobry}
+\seealso{\code{\link{readBins}}.}
+\examples{
+#
+# Check that we can read the 2 exemple files in the seqinR package:
+#
+path1 <- system.file("abif/AmpFLSTR_Panels_v1.txt", package = "seqinr")
+res1 <- readPanels(path1)
+path2 <- system.file("abif/Promega_Panels_v1.txt", package = "seqinr")
+res2 <- readPanels(path2)
+#
+# Show the kits described in res1:
+#
+names(res1)
+#
+# Show some data for a given kit:
+#
+res1[["Identifiler_v1"]][, 1:7]
+#
+# Plot a simple summary of a kit:
+#
+plotPannels <- function(kitname, data){
+  df <- data[[kitname]]
+  dcoln <- unique(as.character(df$dye.col))
+  ncol <- length(dcoln)
+  bmin <- min(df$min.bp)
+  bmax <- max(df$max.bp)
+  plot.new()
+  plot.window(xlim = c(bmin, bmax), ylim = c(0, ncol))
+  rect(bmin, 0, bmax, ncol)
+  yscale <- (ncol-1):0
+  names(yscale) <- dcoln
+  for(i in 1:nrow(df)){
+    col <- as.character(df[i, "dye.col"])
+    rect(df[i, "min.bp"], yscale[col], df[i, "max.bp"], yscale[col]+1, col = col)
+    text(df[i, "min.bp"], yscale[col]+0.5, df[i, "marker"], pos = 4)
+  }
+  title(main = kitname, xlab = "Size [bp]")
+  axis(1)
+}
+
+plotPannels("Identifiler_v1", res1)
+}