findDEgenes: This will perform differential expression using edgeR for...

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This will perform differential expression using edgeR for pairwise comparisons

Usage

findDEgenes(
  input,
  pd = pData(input),
  DEgroup,
  contrastID,
  sizefactor = NULL,
  lib_size = NULL,
  facet_by,
  minCells = 0.1,
  batchID = NULL,
  outdir = "DEresults/",
  outsuffix = "DEresults.tsv",
  pVal = 1,
  contrast = list(c(-1, 1))
)

Arguments

input	Input expression set
pd	pData, optional, by default set to pData of input
DEgroup	a pData variable
contrastID	the condition value from DEgroup to be used as the contrast
sizefactor	a pData column containing the scran reported size factor for each cell
lib_size	a pData column containing the library size for each cell
facet_by	a pData variable to iterate through and perform DE for a condition within each group
minCells	minimum cell fraction the genes should be expressed in to be tested for DE
batchID	a pData variable to use for model accounting for batch effects
outdir	an output directory
outsuffix	an output file suffix
pVal	pvalue cutoff for reported results, by default reports all results
contrast	a list of contrasts to be used for the DE analysis, default is a two-class comparison, with the second class as the comparison class

Details

Utilize information stored in pData to control the DE performed

Examples

findDEgenes(input, pd = selected_table, DEgroup = "genotype", batchID = "beads", facet_by = "cluster", sizefactor="sizefactor", lib_size="lib_size")

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.