upstream_polymerase_ratio: density ratio calculation

Description Usage Arguments Value

View source: R/upstream_density_ratio.R

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

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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/tuSelecter2 documentation built on July 18, 2021, 5:09 p.m.