getCountMatrix

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Description

returns the bam data.frame with an additional column counts. Only relevant if the fasta file used for mapping input was previously collapsed via fastx_toolkit to return a fasta read name in the format of readnumber-totalcounts

Usage

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getCountMatrix(bam_file,pseudo=FALSE)

Arguments

bam_file

An object of class DataFrame (from IRanges). Can be generated from readBam.

pseudo

Logical. If TRUE, assume the reads in the bam file does not have a count record and sets all counts to 1.

Value

An object of class data.frame having the values from the original bam file with an additional 'count' column.

Author(s)

Diana H.P. Low

See Also

readBam

Examples

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