quickCountBam {Rsamtools} | R Documentation |
quickCountBam
groups the records of a BAM file based on their flag
bits and counts the number of records in each group.
quickCountBam(file, ..., param=ScanBamParam(), mainGroupsOnly=FALSE) ## S4 method for signature 'character' quickCountBam(file, index=file, ..., param=ScanBamParam(), mainGroupsOnly=FALSE) ## S4 method for signature 'list' quickCountBam(file, ..., param=ScanBamParam(), mainGroupsOnly=FALSE)
file, index |
For the character method, the path to the BAM file to read, and to the index file of the BAM file to read, respectively. For the list() method, |
... |
Additional arguments, perhaps used by methods. |
param |
An instance of |
mainGroupsOnly |
If |
Nothing is returned. A summary of the counts is printed to the console
unless redirected by sink
.
H. Pages
http://samtools.sourceforge.net/
BamFile
for a method for that class.
bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE) quickCountBam(bamfile)