runPseudoBulk: This function performs pseudobulk analysis on scRNAseq data...

In colin-leeyc/CLpseudobulk: PseudoBulk analysis for scRNAseq

This function performs pseudobulk analysis on scRNAseq data by random sampling

Description

This function performs pseudobulk analysis on scRNAseq data by random sampling

Usage

runPseudoBulk(
  sce,
  cellIDs = NULL,
  obs,
  contrasts,
  replicates = NULL,
  alpha = 0.05
)

Arguments

sce:	SCE object, takes raw counts
cellIDs:	IDs of cells of interest belonging to cluster(s)
obs:	obs/metadata variable to group by - must column name in be in sce colData
replicates:	number of artificial replicates to split each condition into, recommend at least 500 cells per replicate after splitting
contrasts:	DESeq contrast for results - take a vector of 2, eg. c('treatment','control')
alpha:	DESeq alpha parameter (significance level for DE testing)

Value

: list of Pseudobulk raw counts, DESeq2 object, VST-transformed matrix, DE results, colData design table

colin-leeyc/CLpseudobulk documentation built on Nov. 28, 2022, 6:52 p.m.