locusCoverage: Calculate coverage over a given feature

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

Calculate coverage over a given feature

Description

Calculate coverage over a given feature

Usage

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

Arguments

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

Value

coverage of feature

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.