makeAlignmentCountBarPlot: makeAlignmentCountBarPlot

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Make the plot of Multi-Matching Reported in Bam Files.

Usage

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  makeAlignmentCountBarPlot(bamFiles, txtFile="read-alignment-statistics.txt",
                            pairedMode=c("paired", "first", "second"),
                            mc.cores=getThreads())

Arguments

bamFiles

The filenames of input bam files.

txtFile

The filename of output for the summary table.

pairedMode

The pairedMode can be "paired", "first", "second". "paired" will load proper pairs; "first" will load all the first reads; "second" will load all mapped mate reads. This argument is ignored when it's single-end read.

mc.cores

The number of threads to use. By default, we use a internal function NGS:::getThreads to decide.

Details

The barplot gives the number of unmapped reads (If the input read count cannot be retrieved from bam file), the reads that have exactly one hit, the reads that have exactly two hits, and so on.

Value

The object returned by barplot.

Author(s)

Ge Tan

See Also

getBamMultiMatching

Examples

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  bamFile <- system.file("extdata", "bam", "nanocage_ACAGAT_carp_embryo.bam",
                         package="NGS")
  ### Plot the barplot
  makeAlignmentCountBarPlot(bamFile)
  file.remove("read-alignment-statistics.txt")
  

ge11232002/NGS documentation built on May 17, 2019, 12:13 a.m.