quickBamFlagSummary {Rsamtools} | R Documentation |
Group the records of a BAM file based on their flag bits and count the number of records in each group
Description
quickBamFlagSummary
groups the records of a BAM file based on their flag
bits and counts the number of records in each group.
Usage
quickBamFlagSummary(file, ..., param=ScanBamParam(), main.groups.only=FALSE)
## S4 method for signature 'character'
quickBamFlagSummary(file, index=file, ..., param=ScanBamParam(),
main.groups.only=FALSE)
## S4 method for signature 'list'
quickBamFlagSummary(file, ..., param=ScanBamParam(), main.groups.only=FALSE)
Arguments
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 |
main.groups.only |
If |
Value
Nothing is returned. A summary of the counts is printed to the console
unless redirected by sink
.
Author(s)
Hervé Pagès
References
http://samtools.sourceforge.net/
See Also
BamFile
for a method for that class.
Examples
bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
mustWork=TRUE)
quickBamFlagSummary(bamfile)
[Package Rsamtools version 2.18.0 Index]