RNAseqTFValidation: Validate TF Findings with RNA-seq CoGAPS

View source: R/RNAseqTFValidation.R

RNAseqTFValidationR Documentation

Validate TF Findings with RNA-seq CoGAPS

Description

Use results from CoGAPS run on matched RNA-seq data to verify TF activity suggested by motif matching analysis of ATAC CoGAPS output. Uses the fgsea package to find enrichment of PatternMarker genes among genes regulated by identified candidate TFs

Usage

RNAseqTFValidation(
  TFGenes,
  RNACoGAPSResult,
  ATACPatternSet,
  RNAPatternSet,
  matrix = FALSE
)

Arguments

TFGenes

genes regulated by the TFs as returned by simpleMotifTFMatch() or findRegulatoryNetworks()

RNACoGAPSResult

CoGAPSResult object from matched RNA-seq data, or, if matrix = TRUE, a matrix containing patternMarker gene ranks. Must contain gene names

ATACPatternSet

vector of patterns found by CoGAPS in the ATAC data to match against patterns found in RNA

RNAPatternSet

vector of patterns found by CoGAPS in RNA to match against those found in ATAC

matrix

TRUE if inputting matrix of PatternMarker genes, FALSE if inputting CoGAPS result object. FALSE by default

Value

Result matrices from the fgsea function for each pattern comparison

Examples

## Not run: 
gseaList = RNAseqTFValidation(TFMatchResult$RegulatoryNetworks, RNACoGAPS,
 c(1,3), c(2,7), matrix = FALSE)

## End(Not run)

FertigLab/ATACCoGAPS documentation built on June 29, 2022, 4:13 p.m.