summarize_bigwig: Summarize bigwig

In CshlSiepelLab/DENR: Deconvolution of Expression for Nascent RNA Sequencing Data

Description

Summarizes a bigwig over a set of ranges in a GRangesList-class or a GRanges-class object

Usage

summarize_bigwig(
  bigwig_file,
  bins,
  summary_operation = "sum",
  autostyle_seqlevels = TRUE
)

## S4 method for signature 'ANY,GRangesList'
summarize_bigwig(
  bigwig_file,
  bins,
  summary_operation = "sum",
  autostyle_seqlevels = TRUE
)

## S4 method for signature 'ANY,GRanges'
summarize_bigwig(
  bigwig_file,
  bins,
  summary_operation = "sum",
  autostyle_seqlevels = TRUE
)

Arguments

bigwig_file	a string pointing to a bigwig file
bins	A GRangesList-class or GRanges-class object where all elements in a given GRanges (or GRangesList element) are from the same chromosome
summary_operation	the summary opperation to apply per bin (e.g. sum, mean, median, etc.) Defaults to "sum"
autostyle_seqlevels	Logical. If TRUE matches the seqlevel style of the bigwig_file amd bins object. (Default: TRUE)

Value

A list of vectors with each one corresponding to one set of bins and each element of a vector corresponding to a bin

CshlSiepelLab/DENR documentation built on July 16, 2021, 10:42 p.m.