medianExonCoverage: Calculate median values of coverage within exons in rolling...

In McGranahanLab/TcellExTRECT: T cell Exome TREC Tool

Calculate median values of coverage within exons in rolling windows

Description

Calculate median values of coverage within exons in rolling windows

Usage

medianExonCoverage(
  vdj.region.df,
  exons.selected,
  median.k = 50,
  median.thresh = 15,
  exons.to.use
)

Arguments

vdj.region.df	data frame of positions and coverage values
exons.selected	Locations of exons
median.k	rolling median window
median.thresh	threshold to remove exons with low coverage
exons.to.use	option to manually select exons

Value

Data frame of positions and rolling median of coverage values within chosen exons

McGranahanLab/TcellExTRECT documentation built on Jan. 10, 2025, 11:04 p.m.