estimateDEPerCellTypeInner: Differential expression using different methods (DESeq2,...

In kharchenkolab/cacoa: Case-Control Analysis Tools for Single-Cell RNA-Seq

Differential expression using different methods (DESeq2, edgeR, wilcoxon, ttest) with various covariates

Description

Differential expression using different methods (DESeq2, edgeR, wilcoxon, ttest) with various covariates

Usage

estimateDEPerCellTypeInner(
  raw.mats,
  cell.groups = NULL,
  s.groups = NULL,
  ref.level = NULL,
  target.level = NULL,
  common.genes = FALSE,
  cooks.cutoff = FALSE,
  min.cell.count = 10,
  max.cell.count = Inf,
  independent.filtering = TRUE,
  n.cores = 4,
  return.matrix = TRUE,
  fix.n.samples = NULL,
  verbose = TRUE,
  test = "Wald",
  meta.info = NULL,
  gene.filter = NULL
)

Arguments

raw.mats	list of counts matrices; column for gene and row for cell
cell.groups	factor specifying cell types (default=NULL)
s.groups	list of two character vector specifying the app groups to compare (default=NULL)
ref.level	reference level in 'sample.groups', e.g., ctrl, healthy, wt (default=NULL)
target.level	target level in 'sample.groups' (default=NULL)
common.genes	boolean Only investigate common genes across cell groups (default=FALSE)
cooks.cutoff	boolean cooksCutoff for DESeq2 (default=FALSE)
min.cell.count	numeric Minimum cell count (default=10)
max.cell.count	numeric Maximum cell count (default=Inf). If Inf, there is no limit set.
independent.filtering	boolean independentFiltering for DESeq2 (default=FALSE)
n.cores	numeric Number of cores (default=1)
return.matrix	Return merged matrix of results (default=TRUE)
fix.n.samples	Number of samples to fix (default=NULL). If greater the the length of the s.groups, an error is thrown.
verbose	boolean Whether to output verbose messages (default=TRUE)
test	DE method: DESeq2, edgeR, wilcoxon, ttest
meta.info	dataframe with possible covariates; for example, sex or age
gene.filter	matrix/boolean Genes to omit (rows) per cluster (cols) (default=NULL)

Value

differential expression for each cell type

kharchenkolab/cacoa documentation built on Nov. 8, 2024, 6:06 a.m.