applyGREAT: Find Enrichment of GO Terms in PatternMarker Peaks using...

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

Find Enrichment of GO Terms in PatternMarker Peaks using GREAT

Description

Use the rGREAT package to find enrichment of GO terms or genes for the peaks found to be most pattern differentiating using the PatternMarker statistic.

Usage

applyGREAT(
  cogapsResult,
  granges,
  genome,
  scoreThreshold = NULL,
  GREATCategory = "GO"
)

Arguments

cogapsResult	result object from CoGAPS
granges	GRanges object corresponding to the peaks of the scATAC-seq data CoGAPS was applied to
genome	UCSC genome designation for input to the sumbitGreatJob function from the rGREAT package (e.g. "hg19")
scoreThreshold	threshold of PatternMarker score to take peaks for analysis, higher values return more peaks. Defaults to use all PatternMarker genes with value NULL
GREATCategory	input to the category argument of the rGREAT getEnrichmentTables function. Usually "GO" or "Genes"

Value

list containing enrichment results for each pattern

Examples

data("schepCogapsResult")
data(schepGranges)

GOenrichment <- applyGREAT(cogapsResult = schepCogapsResult,
 granges = schepGranges, genome = "hg19")

FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.