Browse code

fixed two bugs reported by Andreas Schoenegger, updated citation information

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@70488 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 13/10/2012 16:48:16
Showing10 changed files

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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 0.7.0
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+Version: 0.7.1
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 Title: Analyze, manage and store bisulfite sequencing data
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 Description: Tools for analyzing and visualizing bisulfite sequencing data
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 Author: Kasper Daniel Hansen
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@@ -193,6 +193,7 @@ setMethod("combine", signature(x = "BSseq", y = "BSseq"), function(x, y, ...) {
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         stop("'x' and 'y' need to be smoothed on the same scale")
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     phenoData <- combine(phenoData(x), phenoData(y))
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     if(identical(granges(x), granges(y))) {
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+        gr <- granges(x)
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         M <- cbind(getBSseq(x, "M"), getBSseq(y, "M"))
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         Cov <- cbind(getBSseq(x, "Cov"), getBSseq(y, "Cov"))
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         if(!hasBeenSmoothed(x) || !hasBeenSmoothed(y)) {
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@@ -60,6 +60,8 @@ getMeth <- function(BSseq, regions = NULL, type = c("smooth", "raw"),
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     }
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     stopifnot(is(BSseq, "BSseq"))
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     type <- match.arg(type)
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+    if(type == "smooth" & !hasBeenSmoothed(BSseq))
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+        stop("'type=smooth' requires the object to have been smoothed.")
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     what <- match.arg(what)
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     z <- abs(qnorm((1 - alpha)/2, mean = 0, sd = 1))
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     if(is.null(regions) && type == "smooth") {
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@@ -336,7 +336,7 @@ read.umtab.chr <- function(files, sampleNames = NULL,
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 read.bsmoothDirRaw <- function(dir, seqnames = NULL, keepCycle = FALSE, keepFilt = FALSE,
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                                header = TRUE, verbose = TRUE) {
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     dir <- normalizePath(dir)
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-    inpattern <- "\\.cpg\\.tsv\\.gz$"
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+    inpattern <- "\\.cpg\\.tsv(|\\.gz)$"
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     if(length(dir) != 1 || !file.info(dir)$isdir)
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         stop("argument 'dir' needs to be a single directory")
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     allChrFiles <- list.files(dir, pattern = inpattern, full.names = TRUE)
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@@ -347,8 +347,12 @@ read.bsmoothDirRaw <- function(dir, seqnames = NULL, keepCycle = FALSE, keepFilt
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         return(NULL)
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     }
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     if(header) {
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-        columnHeaders <- sapply(allChrFiles, function(file) {
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-            out <- readLines(con <- gzfile(file), n = 1)
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+        columnHeaders <- sapply(allChrFiles, function(thisfile) {
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+            if(grepl("\\.gz$", thisfile))
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+                con <- gzfile(thisfile)
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+            else
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+                con <- file(thisfile, open = "r")
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+            out <- readLines(con, n = 1)
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             close(con)
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             out
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         })
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@@ -367,10 +371,14 @@ read.bsmoothDirRaw <- function(dir, seqnames = NULL, keepCycle = FALSE, keepFilt
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         what0[c("Mcy", "Ucy")] <- replicate(2, NULL)
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     if(!keepFilt) 
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         what0[grep("^filt", names(what0))] <- replicate(length(grep("^filt", names(what0))), NULL)
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-    outList <- lapply(allChrFiles, function(file) {
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+    outList <- lapply(allChrFiles, function(thisfile) {
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         if(verbose)
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-            cat(sprintf("Reading '%s'\n", file))
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-        out <- scan(con <- gzfile(file, open = "r"), skip = header, what = what0, sep = "\t",
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+            cat(sprintf("Reading '%s'\n", thisfile))
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+        if(grepl("\\.gz$", thisfile))
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+            con <- gzfile(thisfile)
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+        else
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+            con <- file(thisfile)
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+        out <- scan(con, skip = header, what = what0, sep = "\t",
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                     quote = "", na.strings = "NA", quiet = TRUE)
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         close(con)
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         out
... ...
@@ -6,10 +6,11 @@ bibentry("Article",
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          person(c("Rafael", "A."), "Irizarry")),
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          journal = "Genome Biology",
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          year = 2012,
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-	 note = "In press",  
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-         textVersion = 
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-         paste("KD Hansen, B Langmead, and RA Irizarry",
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-               "BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions", 
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-"Genome Biology, In press (2012)")
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+	 volume = "13",
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+	 pages = "R83",
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+  	 textVersion = 
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+         paste("KD Hansen, B Langmead, and RA Irizarry.",
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+               "BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.", 
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+"Genome Biology, 13:R83 (2012)")
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 )
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@@ -2,6 +2,20 @@
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 \title{bsseq news}
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 \encoding{UTF-8}
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+\section{Version 0.7}{
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+  \itemize{
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+    \item Fixed a bug in getMeth, where type="raw" resulted in an error
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+    for non-smoothed data objects.
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+    \item Updated CITATION and citations in the vignettes.
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+    \item Now read.bsmooth supports both gzipped and non-gzipped files,
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+    whereas previously it assumed the output files to be gzipped.
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+    Thanks to Andreas Schoenegger for reporting this problem.
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+    \item Fixed a bug in combine() that also resulted in a bug in
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+    read.bsmooth when multiple input directories were specified.  Bug
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+    reported by Andreas Schoenegger.
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+  }
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+}
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+
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 \section{Version 0.4}{
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   \itemize{
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     \item Improved combine and fixed a bug.  Also added a non-exported
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@@ -33,6 +33,10 @@ read.bsmooth(dirs, sampleNames = NULL, seqnames = NULL,
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   \item{verbose}{Make the function verbose.}
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 }
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 \note{
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+  Input files can either be gzipped or not.  Gzipping the input files
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+  results in much greater speed of reading (and saves space), so it is
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+  recommended.
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+  
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   We are working on making this function faster and less memory hungry.
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 }
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 \value{
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@@ -19,10 +19,11 @@ options(width=70)
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 \newcommand{\Rpackage}[1]{{\texttt{#1}}}
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 \newcommand{\software}[1]{\textsf{#1}}
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 \newcommand{\R}{\software{R}}
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+\newcommand{\bold}[1]{\textbf{#1}}
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 \title{The bsseq user's guide}
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 \author{Kasper Daniel Hansen \\ \texttt{khansen@jhsph.edu}}
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-\date{Modified: June 20, 2011.  Compiled: \today}
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+\date{Modified: October 13, 2012.  Compiled: \today}
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 \begin{document}
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 \setlength{\parskip}{1\baselineskip}
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 \setlength{\parindent}{0pt}
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@@ -103,6 +104,14 @@ methylation (methylation that is higher in one condition/sample than in another)
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 (methylation that is lower in one condition/sample than in another), and finally differentially
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 methylated position (DMP) referring to a single loci.
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+\subsubsection*{Citation}
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+
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+If you use this package, please cite our BSmooth paper:
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+
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+<<citation,echo=FALSE,results=tex>>=
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+print(citation("bsseq"), style = "latex")
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+@ 
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+
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 \section{Overview}
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 The package assumes that the following data has been extracted from alignments:
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@@ -288,12 +297,12 @@ computed for region-level summary estimates.  Examples
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 <<getMeth>>=
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 getMeth(BS.chr22, regions, type = "raw")
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-getMeth(BS.chr22, regions[2], type = "smooth", what = "perBase")
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+getMeth(BS.chr22, regions[2], type = "raw", what = "perBase")
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 @ 
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 \section{Reading data}
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-\subsubsection{Alignment output from the BSmooth alignment suite}
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+\subsubsection*{Alignment output from the BSmooth alignment suite}
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 It is straightforward to read output files (summarized evidence) from the BSmooth alignment suite,
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 using \Rcode{read.bsmooth}.  This function takes as argument a number of directories, usually
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@@ -301,12 +310,13 @@ corresponding to samples, with the alignment output.  Sometimes, one might want
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 chromosomes, which can be accomplished by the \Rcode{seqnames} argument.  Also, the default values
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 of \Rcode{qualityCutoff = 20} ensures that we do not use methylation evidence with a base quality
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 strictly lower than 20 (since we may not be confident whether the read really supports methylation
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-or not).
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+or not).  The function \Rcode{read.bsmooth} allows for both gzipped and non-gzipped input files. It
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+is faster to read gzipped files, so we recommend gzipping post-alignment.
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 During the development of BSmooth we experimented with a number of different output formats.  These
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 legacy formats can be read with \Rcode{read.umtab} and \Rcode{read.umtab2}.
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-\subsubsection{Alignment output from other aligners}
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+\subsubsection*{Alignment output from other aligners}
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 We are interested in adding additional parsers to the package; if your favorite alignment software
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 is not supported, feel free to get in touch.
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@@ -339,7 +349,7 @@ file may be found by
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 system.file("scripts", "get_BS.chr22.R", package = "bsseq")
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 @ 
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-\section{Analysis}
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+\section*{Analysis}
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 Computing smoothed methylation levels is simple.  We subset \Rcode{BS.chr22} so we only smooth 1
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 sample, for run-time purpose
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@@ -4,7 +4,11 @@
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                   methylated regions}},
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   journal =	 {Genome Biology},
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   year =	 {2012},
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-  note =	 {In press}
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+  volume =	 {13},
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+  number =	 {10},
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+  pages =	 {R83},
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+  doi =		 {10.1186/gb-2012-13-10-r83},
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+  pubmed =	 {23034175}
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 }
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@@ -25,7 +25,7 @@ options(width=70)
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 \title{Analyzing WGBS with the bsseq package}
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 \author{Kasper Daniel Hansen\\ \texttt{khansen@jhsph.edu}}
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-\date{Modified: June 26, 2011.  Compiled: \today}
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+\date{Modified: October 13, 2012.  Compiled: \today}
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 \begin{document}
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 \maketitle
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@@ -62,6 +62,11 @@ BS.cancer.ex
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 pData(BS.cancer.ex)
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 @ 
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+If you use this package, please cite our BSmooth paper
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+<<citation,echo=FALSE,results=tex>>=
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+print(citation("bsseq"), style = "latex")
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+@
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+
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 \section*{Smoothing}
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 The first step of the analysis is to smooth the data