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

Description Usage Arguments Details Examples

View source: R/findDEgenes.R

Description

This will perform differential expression using edgeR for pairwise comparisons

Usage

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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

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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.