ssc.clusterMarkerGene: identify marker genes of each cluster

In Japrin/sscClust: simpler single cell RNAseq data clustering

identify marker genes of each cluster

Description

identify marker genes of each cluster

Usage

ssc.clusterMarkerGene(
  obj,
  assay.name = "exprs",
  ncell.downsample = NULL,
  group.var = "majorCluster",
  batch = NULL,
  assay.bin = NULL,
  out.prefix = NULL,
  n.cores = NULL,
  do.plot = T,
  F.FDR.THRESHOLD = 0.01,
  pairwise.P.THRESHOLD = 0.01,
  pairwise.FC.THRESHOLD = 1,
  use.Kruskal = F,
  method.Max = "mean",
  do.force = F,
  verbose = F,
  ...
)

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")
batch	character; covariate. (default: NULL)
assay.bin	character; binarized expression assay (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)
F.FDR.THRESHOLD	numeric; threshold of the adjusted p value of F-test. (default: 0.01)
pairwise.P.THRESHOLD	numeric; threshold of the adjusted p value of HSD-test (default: 0.01)
pairwise.FC.THRESHOLD	numeric; threshold of the absoute diff of HSD-test (default: 1)
use.Kruskal	logical; whether use Kruskal test for ranking genes (default: FALSE)
method.Max	character; method to find highest group, one of "mean", "median", "rank.mean" (default: mean)
do.force	logical; . (default: FALSE)
verbose	logical; whether output all genes' result. (default: FALSE)
...	parameters passed to findDEGenesByAOV

Details

identify marker genes based on aov and AUC.

Japrin/sscClust documentation built on Dec. 15, 2022, 1:04 p.m.