Calculate coverage over a given feature

Usage

locusCoverage(
  bam_path,
  locus_granges,
  library_strandedness,
  index_suffix = ".bai",
  coverage_threshold = 0,
  ...
)

bam_path

path to a given samples alignment file (.bam)

locus_granges

a granges object for a given gene (or some other feature on only one strand)

library_strandedness

one of c("reverse", "same", "unstranded")

index_suffix

suffix to append to bampath. Default .bai

coverage_threshold

minimum threshold to consider. Default is 0

...

Arguments passed on to strandedScanBamParam

quality_threshold: quality threshold above which reads will be considered. 20l is default, which is chosen b/c it is the default for HTSeq

coverage of feature