get_intron_zc: Read zero coverage data

In pachterlab/kma: KeepMeAround: Intron Retention Detection in RNA-Seq data

Description

Read the zero coverage data otuput into a data.frame.

Usage

get_intron_zc(fname, sample_name, regex = "^chr",
  adjust_method = "bonferroni", rename_target_id = TRUE)

Arguments

fname	a character vector of length one containing the file name
regex	a regular expression to filter from. For intron retention, you usually want to only get the introns. If you want to get everything back, use the regex "*".
adjust_method	the method to use for multiple testing
rename_target_id	if TRUE, rename 'target_id' to 'intron_extension'
exp_name	a character containing the name of the experiment

Value

a data.frame with columns:

intron_extension

the intron_extension coordinates

len

the length of the target

zc_len

the length of the region with zero coverage

zc_pval

the raw p-value under the Poisson model

zc_qval

the corrected p-value using method adjust_method

pachterlab/kma documentation built on May 24, 2019, 5:58 p.m.