motifPatternMatch: Find Motifs and TFs from PatternMarker Peaks

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

Find Motifs and TFs from PatternMarker Peaks

Description

Function that takes CoGAPS result and list of DNA motifs as input and returns motifs which match to the most pattern-defining peaks for each pattern.

Usage

motifPatternMatch(
  cogapsResult,
  generanges,
  motiflist,
  genome,
  scoreThreshold = NULL,
  motifsPerRegion = 1
)

getTFs(motifList, tfData)

findRegulatoryNetworks(TFs, networks)

getTFDescriptions(TFs)

Arguments

cogapsResult	the result object from a CoGAPS run
generanges	GRanges objects corresponding to the genomic regions which form the rows of the ATAC-seq data that CoGAPS was run on
motiflist	a PWMlist of motifs to search the regions for
genome	the ucsc 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 top motifs to return from each peak
motifList	list produced by the motifPatternMatch function
tfData	dataframe of motifs and TFs from cisBP database
TFs	object of TF info returned from the getTFs function
networks	a list of regulatory networks of genes corresponding to TFs; we include humanRegNets and mouseRegNets, downloaded from the TTrust database (Han et al Nucleic Acid Res. 2018)

Value

motifPatternMatch: nested list of the top motif for each region for x number of regions for each pattern

getTFs: list containing list of dataframes of tfData subset to matched TFs and list of how many times each TF was matched to a motif/peak

findRegulatoryNetworks: list of TFs for which we have annotations and the corresponding gene networks for each pattern

getTFDescriptions: list of functional annotations for all TFs in each pattern

Functions

• getTFs: Match motifs to TFs based on the list of motifs returned by motifPatternMatch

• findRegulatoryNetworks: function to match TFs identified by getTFs function to a list of regulatory networks of genes known for those TFs

• getTFDescriptions: function to match functional annotation to a list of TFs from the getTFs function

Examples

data(exampleMotifList)
data(schepGranges)
data(schepCogapsResult)

motifsByPattern = motifPatternMatch(schepCogapsResult, schepGranges,
 exampleMotifList, "hg19")
data(exampleMotifList)
data(schepGranges)
data(schepCogapsResult)
data(tfData)

motifsByPattern = motifPatternMatch(schepCogapsResult, schepGranges, exampleMotifList, "hg19")
motifTFs = getTFs(motifsByPattern, tfData)
data(exampleMotifList)
data(schepGranges)
data(schepCogapsResult)
data(tfData)

motifsByPattern = motifPatternMatch(schepCogapsResult, schepGranges, exampleMotifList, "hg19")
motifTFs = getTFs(motifsByPattern, tfData)

regNets = findRegulatoryNetworks(motifTFs, ATACCoGAPS:::humanRegNets)
data(exampleMotifList)
data(schepGranges)
data(schepCogapsResult)
data(tfData)

motifsByPattern = motifPatternMatch(schepCogapsResult, schepGranges, exampleMotifList, "hg19")
motifTFs = getTFs(motifsByPattern, tfData)

tfDesc = getTFDescriptions(motifTFs)

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