Description Usage Arguments Value Author(s) Examples
Note that the genes/CDS in TopCDSDF are only considered to be suggestions of genes with high expression. For a variety of reasons (e.g. expression of certain CDS may be very rare in some genes), there may not be any expression in any of the bam files for a CDS within a gene. Those CDS will be ignored.
1 | BinCounts(TopCDSDF, PileUpPerFile, NumBins = 100)
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TopCDSDF |
Data frame of CDS returned from select(Homo.sapiens). |
PileUpPerFile |
List of Rsamtools pileups per file returned from GetPileUpPerGene(). |
NumBins |
Number of bins to use when parsing the counts for each gene. Default value is 100. |
A list of the median, mean, and 3rd quartile bin counts.
Nathaniel J. Madrid, Jason Byars
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | BamFilePaths <- dir(path="/home/ubuntu/BamFiles", pattern=".*.bam$", full.names=T)
TopGenesDF <- data.frame(gene = c("NM_016824", "NM_019903", "NP_001112"))
cdsColumns <- c("CDSCHROM", "CDSSTART", "CDSEND", "CDSSTRAND", "SYMBOL")
TopCDSDF <- select(Homo.sapiens, keys=as.character(TopGenesDF$gene), columns=cdsColumns, keytype="REFSEQ")
TopCDSDF$CDSCHROM <- sub("chr", "", TopCDSDF$CDSCHROM)
TopCDSDF <- TopCDSDF[which(TopCDSDF$CDSCHROM %in% c(1:22, "X", "Y")), ]
# BIN THE COUNTS
PileUpPerFile <- lapply(BamFilePaths[1:3], function(f) GetPileUpPerGene(f, TopCDSDF))
BinnedCounts <- BinCounts(TopCDSDF, PileUpPerFile, NumBins=100)
BinnedCountsMedian <- BinnedCounts[[1]]
BinnedCountsMean <- BinnedCounts[[2]]
BinnedCounts3rdQ <- BinnedCounts[[3]]
# CREATE PLOTS
g <- ggplot(BinnedCountsMedian, aes(x=BinID, y=RescaledCount, color=FileID)) + geom_line()
g <- g + ylab(label="Normalized Read Coverage") + xlab("Normalized Distance Along Transcript 5' -> 3' (%)")
g <- g + ggtitle(paste(format(length(unique(TopGenesDF$gene)), big.mark=","), " Genes", sep=""))
g
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