exonsTcellExTRECT: Function to run T cell ExTRECT and return data frame

In McGranahanLab/TcellExTRECT: T cell Exome TREC Tool

Function to run T cell ExTRECT and return data frame

Description

Function to run T cell ExTRECT and return data frame

Usage

exonsTcellExTRECT(
  vdj.region.df,
  exons.selected,
  vdj.seg,
  hg19_or_38 = "hg19",
  exons.to.use = NULL,
  GC_correct = TRUE,
  median.k = 50,
  median.thresh = 15,
  summariseExons = TRUE
)

Arguments

vdj.region.df	data frame containing coverage values by position
exons.selected	list of exon positions based on exome capture kit used
vdj.seg	locations of segments used for calculation of TCRA score
hg19_or_38	hg19 or hg38 version of genome
exons.to.use	option to manually select which exons to use (defaults to all)
GC_correct	whether to use GC correction or not for output
median.k	rolling median window
median.thresh	threshold to remove exons with low coverage
summariseExons	whether or not to summarise by exons (median)

Value

data frame of TCRA T cell fractions with 95% CI

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