edgeRDE: This will run edgeR to find differentially expressed genes....

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

Description

This will run edgeR to find differentially expressed genes. Use the wrapping functions findDEgenes or findDEmarkers to use pData columns and get the proper input

Usage

edgeRDE(
  input,
  groups,
  batch,
  sizefactor,
  lib_size,
  minCells,
  pVal = 1,
  contrast = list(c(-1, 1))
)

Arguments

input	Input expression set
groups	an integer vector with the group for each cell
batch	a vector with the batch for each cell, if you don't need batches create a vector with the same id for all cells
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
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 The result is a list with the contrast results, access each element for the DE table

Examples

myDEresults = edgeRDE(input, groups = mygroup, batch = beads, sizefactor = "sizefactor", lib_size = "lib_size")

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