model_agreement: Computes GOF statistic for groups of transcripts

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

Description

Annotates transcriptes from the input GRangesList-class object with two additional columns: percent_match and percent_transcribed. Within the genomic interval covered by each group of transcripts, certain bases are predicted to be transcribed or not for each transcript annotation. Based on the supplied bigwigs each base in the relevant region is then annotated as containig polymerase (being transcribed) or not. percent_match is the fraction of bases whose state, as predicted by the transcript annotations matches the annotation from the data. percent_transcribed is then the percent of the region predicted by the transcript annotation to be transcribed that actually is.

Usage

model_agreement(tx_grps, bigwig_plus, bigwig_minus)

Arguments

tx_grps	a GRangesList-class object that contains groups of overlapping transcripts
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

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