calTissueDist: calculate Startrac.dist (tissue distribution preference)

In Japrin/STARTRAC: Single T-cell Analysis by Rna-seq and Tcr TRACking

calculate Startrac.dist (tissue distribution preference)

Description

calculate Startrac.dist (tissue distribution preference)

Usage

calTissueDist(
  dat.tb,
  byPatient = F,
  colname.cluster = "majorCluster",
  colname.patient = "patient",
  colname.tissue = "loc",
  method = "chisq",
  min.rowSum = 0
)

Arguments

dat.tb	data.frame. Each line for a cell, and these columns as required: 'majorCluster', 'loc'
byPatient	logical. whether calculate the index for each patient. (default: FALSE)
colname.cluster	character. which column specify the cluster (default: "majorCluster")
colname.patient	character. which column specify the patient (default: "patient")
colname.tissue	character. which column specify the tissue (default: "loc")
method	character. method to use, one of "chisq", "fisher", and "freq" (default: "chisq")
min.rowSum	integer. rows with rowSum <= this value will be filtered out (default: 0)

Details

calculate Startrac.dist (tissue distribution preference).

Value

an array full of R_o/e (method="chisq") or list with components of OR, p.value etc. from fisher.test (method="fisher")

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