Browse code

moved to a SummarizedExperiment backend for class 'BSseq'

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78143 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 06/07/2013 21:26:40
Showing 1 changed files
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@@ -37,7 +37,7 @@ read.umtab2(dirs, sampleNames = NULL, rmZeroCov = FALSE,
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 }
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 \value{
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   Both functions returns lists, the components are
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-  \item{BSdata}{An object of class \code{"BSseq"} containing the
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+  \item{BSdata}{An object of class \code{BSseq} containing the
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     methylation evidence.}
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   \item{GC}{A vector of local GC content values.}
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   \item{Map}{A vector of local mapability values.}
Browse code

Adds bsseq and DBCiP to the repos.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@67929 bc3139a8-67e5-0310-9ffc-ced21a209358

m.carlson authored on 20/07/2012 17:45:09
Showing 1 changed files
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new file mode 100644
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@@ -0,0 +1,76 @@
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+\name{read.umtab}
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+\alias{read.umtab}
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+\alias{read.umtab2}
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+\title{
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+  Parsing UM tab files (legacy output) containing output from the
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+  BSmooth aligner. 
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+}
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+\description{
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+  Parsing UM tab files containing output from the bisulfite aligner
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+  \code{Merman}.  This is two different legacy formats, which we keep
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+  around.  These functions are likely to be deprecated in the future.
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+}
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+\usage{
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+read.umtab(dirs, sampleNames = NULL, rmZeroCov = FALSE,
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+  pattern = NULL, keepU = c("U10", "U20", "U30", "U40"),
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+  keepM = c("M10", "M20", "M30", "M40"), verbose = TRUE)
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+
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+read.umtab2(dirs, sampleNames = NULL, rmZeroCov = FALSE,
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+  readCycle = FALSE, keepFilt = FALSE,
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+  pattern = NULL, keepU, keepM, verbose = TRUE)
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+}
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+\arguments{
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+  \item{dirs}{Input directories.  Usually each sample is in a different
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+    directory.} 
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+  \item{pattern}{An optional pattern, see \code{list.files} in the base
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+    package.} 
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+  \item{sampleNames}{sample names, based on the order of \code{dirs}.}
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+  \item{rmZeroCov}{Should methylation loci that have zero coverage in
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+    all samples be removed.  This will result in a much smaller object
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+    if the data originates from (targeted) capture bisulfite
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+    sequencing.} 
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+  \item{keepU}{A vector of U columns which are kept.}
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+  \item{keepM}{A vector of M columns which are kept.}
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+  \item{readCycle}{Should the cycle columns be returned?}
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+  \item{keepFilt}{Should the filter columns be returned?}
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+  \item{verbose}{Make the function verbose.}
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+}
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+\value{
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+  Both functions returns lists, the components are
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+  \item{BSdata}{An object of class \code{"BSseq"} containing the
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+    methylation evidence.}
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+  \item{GC}{A vector of local GC content values.}
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+  \item{Map}{A vector of local mapability values.}
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+  \item{Mcy}{A matrix of the number of unique M cycles.}
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+  \item{Ucy}{A matrix of the number of unique U cycles.}
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+  \item{chr}{A vector of chromosome names.}
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+  \item{pos}{A vector of genomic positions.}
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+  \item{M}{A matrix representing methylation evidence.}
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+  \item{U}{A matrix representing un-methylation evidence.}
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+  \item{csums}{Description of 'comp2'}
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+}
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+\details{
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+  \code{read.umtab2} is newer than \code{read.umtab} and both process
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+  output from older versions of the BSmooth alignment suite (versions
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+  older than 0.6.1).  These functions are likely to be deprecated in the
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+  future.  Newer output from the BSmooth alignment suite can be parsed
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+  using \code{read.bsmooth}.
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+
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+  A script using this function can be found in the \code{bsseqData}
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+  package, in the file \file{scripts/create_BS.cancer.R}.
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+}
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+\author{
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+  Kasper Daniel Hansen \email{khansen@jhsph.edu}
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+}
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+\seealso{
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+  \code{\link{read.bsmooth}}.
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+}
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+\examples{
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+\dontrun{
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+require(bsseqData)
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+umDir <- system.file("umtab", package = "bsseqData")
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+sampleNames <- list.files(umDir)
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+dirs <- file.path(umDir, sampleNames, "umtab")
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+umData <- read.umtab(dirs, sampleNames)
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+}
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+}