inSilico.TCell: Identification of T cells (simple average-threshold method)
In Japrin/scPip: pipeline for scRNA-seq data analysis

inSilico.TCell

R Documentation

Identification of T cells (simple average-threshold method)

Description

Identification of T cells (simple average-threshold method)

Usage

inSilico.TCell(
  obj,
  out.prefix,
  assay.name = "norm_exprs",
  vis.v = c(0.25, 0.5),
  Th.CD3 = 0.25,
  Th.CD8 = 0.5,
  Th.CD4 = 0.5,
  Th.TH = 0.25,
  Th.TR = 0.25,
  do.zscore = F,
  Th.DC = 0.25,
  Th.GC1 = 0.25,
  Th.GC2 = 0.25,
  do.rescue = T
)

Arguments

`obj`	object of `SingleCellExperiment` or `AnnDataR6`
`out.prefix`	character; output prefix. (default: NULL)
`assay.name`	character vector; which assay to use. (default: "norm_exprs").
`vis.v`	double vector; for vertical lines in visulization. (default: c(0.25,0.5)).
`Th.CD3`	double; threshold for T cell signature (mean of CD3D, CD3G). (default: 0.25)
`Th.CD8`	double; threshold for CD8 (mean of CD8A, CD8B). (default: 0.25)
`Th.CD4`	double; threshold for CD4 (expression of CD4). (default: 0.25)
`Th.TH`	double; threshold for Thelper signature (mean of CD4, CD40LG). (default: 0.25)
`Th.TR`	double; threshold for Treg signature (mean of CD4, FOXP3). (default: 0.25)
`do.zscore`	logical; whether use zscore for calculation. (default: FALSE)
`Th.DC`	double; threshold for delta receptor constant chain. (default: 0.25)
`Th.GC1`	double; threshold for gamma receptor constant chain 1. (default: 0.25)
`Th.GC2`	double; threshold for gamma receptor constant chain 2. (default: 0.25)
`do.rescue`	logical; whether use "rescue" mode. (default: FALSE)