ssc.DEGene.limma: identify differential genes of each cluster (comparing the...

In Japrin/sscClust: simpler single cell RNAseq data clustering

identify differential genes of each cluster (comparing the cluster with all others), using limma

Description

identify differential genes of each cluster (comparing the cluster with all others), using limma

Usage

ssc.DEGene.limma(
  obj,
  assay.name = "exprs",
  ncell.downsample = NULL,
  group.var = "majorCluster",
  group.list = NULL,
  group.mode = "multi",
  batch = NULL,
  out.prefix = NULL,
  n.cores = NULL,
  do.plot = T,
  T.fdr = 0.01,
  T.logFC = 1,
  T.expr = 0.3,
  T.bin.useZ = T,
  verbose = 1,
  do.force = F,
  method = "limma"
)

Arguments

obj	object of singleCellExperiment class
assay.name	character; which assay (default: "exprs")
ncell.downsample	integer; for each group, number of cells downsample to. (default: NULL)
group.var	character; column in the colData(obj) used for grouping. (default: "majorCluster")
group.list	character; DEG of groups to calculate. If NULL, all groups. (default: "NULL")
group.mode	character; One of "multi", "multiAsTwo" (default: "multi")
batch	character; covariate. (default: NULL)
out.prefix	character; output prefix. (default: NULL)
n.cores	integer; number of cores used, if NULL it will be determined automatically (default: NULL)
do.plot	logical; whether plot. (default: TRUE)
T.fdr	numeric; threshold of the adjusted p value of moderated t-test (default: 0.05)
T.logFC	numeric; threshold of the absoute diff (default: 1)
T.expr	numeric; threshold for binarizing exprs (default: 0.3)
T.bin.useZ	logical; wheter use the z-score version of assay.namme for binarizing exprs (default: T)
verbose	integer; verbose level. (default: 1)
do.force	logical; . (default: FALSE)
method	character; . (default: "limma")

Details

identify differential genes using limma

Japrin/sscClust documentation built on March 1, 2025, 11:40 a.m.