Browse code

Added read.bismark function, along with documentation and example dataset for this function.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@71341 bc3139a8-67e5-0310-9ffc-ced21a209358

Peter Hickey authored on 19/11/2012 22:53:38
Showing7 changed files

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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 0.7.2
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+Version: 0.7.3
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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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@@ -8,8 +8,8 @@ Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges,
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         parallel, matrixStats
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 Imports: scales, stats, graphics, Biobase, locfit
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 Suggests: RUnit, bsseqData
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-Collate: hasGRanges.R BSseq_class.R BSseq_utils.R utils.R read.R
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-        BSmooth.R dmrFinder.R gof_stats.R plotting.R fisher.R fixes.R
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+Collate: hasGRanges.R BSseq_class.R BSseq_utils.R utils.R read.bsmooth.R
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+        read.bismark.R BSmooth.R dmrFinder.R gof_stats.R plotting.R fisher.R fixes.R
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 License: Artistic-2.0
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 LazyData: yes
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 biocViews: DNAMethylation
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@@ -60,7 +60,7 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
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        "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
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        "combineList",
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        "plotRegion", "plotManyRegions", 
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-       "read.umtab", "read.umtab2", "read.bsmooth",
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+       "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
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        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
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        "data.frame2GRanges", "BSseqTstat")
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new file mode 100644
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@@ -0,0 +1,69 @@
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+read.bismark <- function(files, sampleNames, returnRaw = FALSE, rmZeroCov = FALSE, verbose = TRUE){
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+  ## Argument checking
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+  if (anyDuplicated(files)){
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+    stop("duplicate entries in 'files'")
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+  }
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+  if (length(sampleNames) != length(files) | anyDuplicated(sampleNames)){
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+    stop("argument 'sampleNames' has to have the same length as argument 'files', without duplicate entries")
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+  }
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+  ## Process each file
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+  idxes <- seq_along(files)
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+  names(idxes) <- sampleNames
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+  allOut <- lapply(idxes, function(ii){
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+    if (verbose) {
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+      cat(sprintf("Reading file '%s' ... ", files[ii]))
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+    }
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+    stime <- system.time({
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+      if (returnRaw) {
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+        out <- read.bismarkFileRaw(thisfile = files[ii])
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+      } else{
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+        raw <- read.bismarkFileRaw(thisfile = files[ii])
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+        M <- matrix(elementMetadata(raw)[, "mCount"], ncol = 1)
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+        Cov <- M + elementMetadata(raw)[, "uCount"]
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+        elementMetadata(raw) <- NULL
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+        out <- BSseq(gr = raw, M = M, Cov = Cov, sampleNames = sampleNames[ii], rmZeroCov = rmZeroCov)
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+      }
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+    })[3]
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+    if (verbose) {
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+      cat(sprintf("in %.1f secs\n", stime))  
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+    }
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+    out  
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+  })
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+  if (!returnRaw) {
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+    if (verbose) {
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+      cat(sprintf("Joining samples ... "))
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+    }
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+    stime <- system.time({
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+      allOut <- Reduce("combine", allOut)
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+    })[3]
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+    if (verbose) {
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+      cat(sprintf("in %.1f secs\n", stime))
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+    }
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+  }
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+  allOut
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+}
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+
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+read.bismarkFileRaw <- function(thisfile, verbose = TRUE){
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+  ## Set up the 'what' argument for scan()
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+  columnHeaders <- c("chr", "start", "end", "mPerc", "mCount", "uCount")
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+  what0 <- replicate(length(columnHeaders), character(0))
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+  names(what0) <- columnHeaders
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+  int <- which(columnHeaders %in% c("start", "end", "mCount", "uCount"))
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+  what0[int] <- replicate(length(int), integer(0))
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+  dbl <- which(columnHeaders %in% "mPerc")
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+  what0[dbl] <- replicate(length(dbl), double(0))
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+  ## Read in the file
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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 <- scan(file = con, what = what0, sep = "\t", quote = "", na.strings = "NA", quiet = TRUE)
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+  close(con)
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+  ## Create GRanges instance from 'out'
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+  gr <- GRanges(seqnames = out[["chr"]], ranges = IRanges(start = out[["start"]], width = 1))
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+  out[["chr"]] <- out[["start"]] <- out[["end"]] <- NULL
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+  out <- out[!sapply(out, is.null)]
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+  df <- DataFrame(out)
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+  elementMetadata(gr) <- df
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+  gr
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+}
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similarity index 100%
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rename from R/read.R
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rename to R/read.bsmooth.R
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new file mode 100644
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