Startrac.run: warpper function for Startrac analysis
In Japrin/STARTRAC: Single T-cell Analysis by Rna-seq and Tcr TRACking

Startrac.run

R Documentation

warpper function for Startrac analysis

Description

warpper function for Startrac analysis

Usage

Startrac.run(cell.data, proj = "CRC", cores = NULL, n.perm = NULL, verbose = 0)

Arguments

`cell.data`	data.frame. Each line for a cell, and these columns as required: 'Cell_Name', 'clone.id', 'patient', 'majorCluster', 'loc'
`proj`	character. String used to annotate the project.
`cores`	integer. number of core to be used. default: NULL.
`n.perm`	integer. number of permutation will be performed. If NULL, no permutation. (default: NULL)
`verbose`	integer. verbose level indicate how to include intermediate result (some Startrac objects)

Details

run the Startrac pipeline

Value

an list contains data.frame elements "cluster.data","pIndex.migr" and "pIndex.tran"

Examples

library("Startrac")
dat.file <- system.file("extdata/example.cloneDat.Zhang2018.txt",package = "Startrac")
in.dat <- read.table(dat.file,stringsAsFactors = FALSE,head=TRUE)
out <- Startrac.run(in.dat, proj="CRC", cores=2,verbose=FALSE)

Japrin/STARTRAC documentation built on Dec. 4, 2023, 1:35 a.m.