convertLimmaToSCE: convert the limma result to gene by meta-cluster data stored...

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

convert the limma result to gene by meta-cluster data stored in an SingleCellExperiment object

Description

convert the limma result to gene by meta-cluster data stored in an SingleCellExperiment object

Usage

convertLimmaToSCE(
  de.limma.tb,
  out.prefix,
  ncores = 8,
  min.ncells = 30,
  min.ncellsStudy = 200,
  gset.list = NULL,
  direct.sig = T,
  TH.gene.occ = 1,
  de.mode = "multiAsTwo",
  column.exp = "meanScale",
  gene.used = NULL,
  colSet = list()
)

Arguments

de.limma.tb	data.table; one line for a dataset. columns "data.id", "platform", and "dfile" are required
out.prefix	character; output prefix
ncores	integer; number of CPU cores to use. (default: 8)
min.ncells	integer; only meta-clusters with number of cells > min.ncells are used. (default: 30)
min.ncellsStudy	integer; only datasets with number of cells > min.ncellsStudy are used. (default: 200)
gset.list	list; list containing gene sets. (default: NULL)
direct.sig	logical; if TRUE, genes exibit significance in all datasets will be assigned "sig" directly, irrespective of combined ES and combined adjusted p vlaue. (default: TRUE)
TH.gene.occ	double; range from 0 to 1. genes present in >= TH.gene.occ datasets are used. (default: 1)
de.mode	character; mode of differential expression analysis. (default: "multiAsTwo")
column.exp	character; convert the column of limma result to assay data. (default: "meanScale")
gene.used	character; only keep genes in gene.used. (default: NULL)
colSet	list; mapping iterms in the names to colors in the values. (default: list())

Details

convert the limma result to gene by meta-cluster data stored in an SingleCellExperiment object

Value

a SingleCellExperiment object

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