cal.signatureScore.gdT.Fred: Identification of gamma delta T cells (Fred's method)

In Japrin/scPip: pipeline for scRNA-seq data analysis

Identification of gamma delta T cells (Fred's method)

Description

Identification of gamma delta T cells (Fred's method)

Usage

cal.signatureScore.gdT.Fred(
  obj,
  GSx = c("CD3D", "CD3E", "TRDC", "TRGC1", "TRGC2"),
  GSy = c("CD8A", "CD8B"),
  col.name = "Score.gammaDeltaT",
  th.score = 0.35,
  out.prefix = NULL
)

Arguments

obj	object of SingleCellExperiment; assay "counts" is required.
GSx	character vector; gdT marker gene list. (default: c("CD3D","CD3E","TRDC","TRGC1","TRGC2")).
GSy	character vector; CD8 T cell marker gene list. (default: c("CD8A","CD8B")).
col.name	character; prefix of column names, to be added to obj. (default: "Score.gammaDeltaT")
th.score	double; threshold of the score. (default: 0.35)
out.prefix	character; output prefix. (default: NULL)

Value

a SingleCellExperiment object

Japrin/scPip documentation built on Jan. 29, 2024, 1:20 a.m.