collect_tss_features: Generate GRangesList of windows

Description Usage Arguments Value

View source: R/tss_predictor.R

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

1
2
3
4
5
6
7
8
9
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/tuSelecter2 documentation built on July 18, 2021, 5:09 p.m.