Rsamtools: quickBamFlagSummary – R documentation

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quickBamFlagSummary

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, `file` is a named list with elements “qname” and “flag” with content as from `scanBam`.
`...`	Additional arguments, perhaps used by methods.
`param`	An instance of `ScanBamParam`. This determines which records are considered in the counting.
`main.groups.only`	If `TRUE`, then the counting is performed for the main groups only.

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/

Examples

bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                       mustWork=TRUE)
quickBamFlagSummary(bamfile)

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release