findDEmarkers: This will perform differential expression using edgeR to find...

Description Usage Arguments Details Examples

View source: R/findDEmarkers.R

Description

This will perform differential expression using edgeR to find markers for each cluster or group compared to all others

Usage

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findDEmarkers(
  input,
  pd = NULL,
  DEgroup,
  sizefactor = NULL,
  lib_size = NULL,
  batchID = NULL,
  outdir = "DEmarkers/",
  outsuffix = "DEmarkers.tsv",
  minCells = 0.01,
  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

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

batchID

a pData variable to use for model accounting for batch effects

outdir

an output directory

outsuffix

an output file suffix

minCells

minimum cell fraction the genes should be expressed in to be tested for DE

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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findDEmarkers(input, pd = selected_table, DEgroup = "cluster", batchID = "beads", sizefactor="sizefactor", lib_size="lib_size")

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