get_coverage: Get coverage from bigwig file(s) across a region of interest

In dzhang32/RNAdiagnosR: What the Package Does (One Line, Title Case)

Description

get_coverage

Usage

get_coverage(bw_paths, region_of_interest = NULL, normalise = F,
  sum_func = mean, gene_name = NULL, ref = NULL, change_chr = F,
  ...)

Arguments

bw_paths	chr. bigwig file path(s) from which to obtain coverage
region_of_interest	gr. A genomic range of length 1. If NULL, will use the gene start and end.
normalise	lgl. if TRUE will normalise using the coverage over reduced exons of the gene.
sum_func	func. Any function to summarise numeric values. Defaults to mean.
gene_name	chr. Gene symbol, will use to obtain region_of_interest and normalise to reduced exons definitions.
ref	gr. gtf annotation imported through rtracklayer.
change_chr	lgl. Add "chr" to start of seqlevels to match the bw format?
...	additional arguments to pass into the sum_func

Value

tibble with the columns detailing chromosome, position (1 for every base in region_of_interest) and normalised coverage

dzhang32/RNAdiagnosR documentation built on Dec. 5, 2019, 2 a.m.