iteratePseudoBulk: This function iterates 'pseudobulk' DE analysis using DESeq2...

In colin-leeyc/CLpseudobulk: PseudoBulk analysis for scRNAseq

This function iterates 'pseudobulk' DE analysis using DESeq2 pipeline \ on scRNAseq data for genes of interest. It is essentially bootstrapping for scRNAseq pseudobulk analysis.

Description

This function iterates 'pseudobulk' DE analysis using DESeq2 pipeline \ on scRNAseq data for genes of interest. It is essentially bootstrapping for scRNAseq pseudobulk analysis.

Usage

iteratePseudoBulk(
  sce,
  cellIDs = NULL,
  obs,
  contrasts,
  replicates = NULL,
  alpha = 0.05,
  genes = NULL,
  iterations = 10
)

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
contrast:	DESeq contrast for results - take a vector of 2, eg. c('treatment','control')
alpha:	significance level
genes:	vector of genes of interest, if NULL, iterate and test for all
iterations:	number of times to permute random sampling and results function

Value

A list of LogFoldChange, adjusted P value, and p value statistics for genes of interest

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