upstream_polymerase_ratio: density ratio calculation

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

Description

Calculates the log2 ratio of the polymerase upstream and downstream of the TSS on the sense strand. This ratio is used to determine if a transcript may be active. Used during data addition to determine if a transcript specified as inactive in the fit call should be overriden.NOTE: ratio is calculated with an additional 1 pseudocount/kb added to the numerator and denominator

Usage

upstream_polymerase_ratio(
  tq,
  bigwig_plus,
  bigwig_minus,
  up_width = 5000,
  up_shift = 500,
  body_width = 5000,
  body_shift = 500
)

Arguments

tq	A transcript_quantifier-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
up_width	The length of the region upstream of the TSS to calculate the polymerase denisty in
up_shift	how far upstream of the TSS up_width is shifted
body_width	The length of the region downstream of the TSS to calculate the polymerase denisty in
body_shift	how far downstream of the TSS body_width is shifted

Value

a named vector of the polymerase ratios

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