View source: R/countBamInGranges.R
getBamCounts | R Documentation |
Essentially a wrapper for the accessory function countBamInGRanges which only considers a single BAM file at a time.
getBamCounts( bed.frame = NULL, bed.file = NULL, bam.files, index.files = bam.files, min.mapq = 20, read.width = 300, include.chr = FALSE, referenceFasta = NULL )
bed.frame |
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bed.file |
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bam.files |
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index.files |
Optional |
min.mapq |
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read.width |
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include.chr |
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referenceFasta |
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This function is largely a copy of a similar one available in the exomeCopy package.
A GenomicRanges object that stores the read count data for the BAM files listed as argument.
Vincent Plagnol
exomeCopy R package.
data(exons.hg19) exons.hg19.RHD <- subset(exons.hg19, grepl(pattern = '^RHD', exons.hg19[['name']])) minimum_bam_file <- system.file('extdata/minimum_1_25630000_25650000.bam', package = 'ExomeDepth') my_counts <- getBamCounts(bed.frame = exons.hg19.RHD, bam.files = minimum_bam_file) print(my_counts)
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