addInputReadCounts: addInputReadCounts

Description Usage Arguments Value Author(s) Examples

Description

Add the number of input reads as a comment to the header of bamFile.

Usage

1
  addInputReadCounts(bamFiles, reads1s, binary = "samtools")

Arguments

bamFiles

The filenames of input bam files.

reads1s

The filenames of the corresponding input fastq files.

binary

The name/filename of the binary "samtools" to call.

Value

The filenames of input bam files.

Author(s)

Ge Tan

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
  
  ## This example is not tested because it requires external software "samtools"
  bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                         mustWork=TRUE)
  tempBamFile <- tempfile(fileext=".bam")
  file.copy(bamfile, tempBamFile)
  reads1 <- file.path(system.file("extdata", package="NGS"), "fastq",
                      "nanocage_ACAGAT_carp_embryo_R1.fastq")
  addInputReadCounts(bamFiles=tempBamFile, reads1s=reads1, binary="samtools")
  file.remove(tempBamFile)
  

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