collect_tss_features: Generate GRangesList of windows

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

Description

Generates a set of windows for each transcript in a GRanges-class object. Uses the TSS of each region as the 0th co-ordinate in generating windows.

Usage

collect_tss_features(
  transcripts,
  bigwig_plus,
  bigwig_minus,
  bins = 21L,
  bin_width = 51L,
  remove_incomplete = TRUE,
  remove_all_zero = FALSE
)

Arguments

transcripts	a GRanges-class object
bigwig_plus	the path to a bigwig for reads on the plus strand
bigwig_minus	the path to a bigwig for reads on the minus strand
bins	a single value or vector of length equal to bin_width indicating the number of bins to generate, with the central bin centered on the focal site, must be odd
bin_width	a vector of one or more odd valued integers indicating the width of the bins to be generated. If multiple value are specified, windows are generated for all sizes specified
remove_incomplete	remove regions where any window features go outside the chromosomal range
remove_all_zero	remove TSS that have only 0 values in their feature vector

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.