label_transcripts: Generate training labels for TSS

In CshlSiepelLab/tuSelecter2: Deconvolution of Expression for Nascent RNA Sequencing Data

Description

Labels active TSS from by generating an empirical distribution of *-cap sequencing count data across all TSS and labeling the upper tail as active and sites with no *-cap data as inactive.

Usage

label_transcripts(
  transcripts,
  cap_bigwig_plus,
  cap_bigwig_minus,
  ctrl_bigwig_plus,
  ctrl_bigwig_minus,
  ctrl_cdf_alpha = 0.01,
  radius = 150
)

Arguments

transcripts	transcripts a GRanges-class that holds all the transcript coordinates
cap_bigwig_plus	PRO-cap/GRO-cap data from plus strand
cap_bigwig_minus	PRO-cap/GRO-cap data from minus strand
ctrl_bigwig_plus	PRO-seq/GRO-seq data from plus strand
ctrl_bigwig_minus	PRO-seq/GRO-seq data from minus strand
ctrl_cdf_alpha	foo
radius	The radius around the TSS in which to collect counts

Value

Return transcripts with an added active_tss column indicating if the tss is active

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