simpleMotifTFMatch: Motif/TF Matching in a Single Function

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

Motif/TF Matching in a Single Function

Description

If the user does not have a specific set of motifs, transcription factors, or regulatory networks that they want to match against, simply uses the core motifs from the JASPAR database to find motifs and TFs in the most Pattern differentiating peaks, as well as regulatory networks from TTrust database corresponding to the identified TFs. This is used to provide transcription factors with functional annotation which may suggest plausible unknown regulatory mechanisms operating in the cell types of interest within the data.

Usage

simpleMotifTFMatch(
  cogapsResult,
  generanges,
  organism,
  genome,
  scoreThreshold = NULL,
  motifsPerRegion = 1
)

Arguments

cogapsResult	result object from CoGAPS run
generanges	GRanges object corresponding to peaks in ATACseq data CoGAPS was run on
organism	organism name (e.g. "Homo sapiens")
genome	genome version to use (e.g. hg19, mm10)
scoreThreshold	threshold for the most pattern defining peaks as per the PatternMarker statistic from the CoGAPS package. By default is NULL, in which case all Pattern defining peaks will be used for motif matching. Used to reduce compute time, as results are quite robust across thresholds
motifsPerRegion	number of motifs to attempt to find within each peak

Value

list containing list of matched motifs, list of transciption factors, regulatory gene networks known for those TFs, functional annotations, summary showing how many times each TF was matched to a peak, and the downloaded set of motifs for the user to save for reproducibility

Examples

data("schepCogapsResult")
data(schepGranges)

motifResults = simpleMotifTFMatch(cogapsResult = schepCogapsResult,
 generanges = schepGranges, organism = "Homo sapiens",
 genome = "hg19", motifsPerRegion = 1)

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