runTcellExTRECT: Function to run T cell ExTRECT

In McGranahanLab/TcellExTRECT: T cell Exome TREC Tool

Function to run T cell ExTRECT

Description

Function to run T cell ExTRECT

Usage

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

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
sample_name	name of sample run

Value

data frame of TCRA T cell fractions with 95% CI and QC fit value for quality of the solution

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