prepareCoverageGC {MADSEQ} | R Documentation |
Given a bam file and a bed file containing targeted regions, return sequencing coverage and GC content for each targeted region
prepareCoverageGC(target_bed, bam, genome_assembly = "hg19")
target_bed |
A |
bam |
character, path to the bam file. Please make sure that bam file is sorted, and the index bam is present |
genome_assembly |
A |
a GRanges object with at least two mcols: depth and GC, each range indicating a targeted region
The bam file should be sorted and indexed.
Yu Kong
## specify the path to the location of bed file target = system.file("extdata","target.bed",package="MADSEQ") ## specify the path to the bam file aneuploidy_bam = system.file("extdata","aneuploidy.bam",package="MADSEQ") normal_bam = system.file("extdata","normal.bam",package="MADSEQ") ## prepare coverage data for the samples aneuploidy_cov_gc = prepareCoverageGC(target,aneuploidy_bam,"hg19") normal_cov_gc = prepareCoverageGC(target,normal_bam,"hg19")