findSupportingRemapPeaks: Find Corresponding TF Binding From The ReMap2022 Project

In Simon-Coetzee/motifBreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

Find Corresponding TF Binding From The ReMap2022 Project

Description

Find Corresponding TF Binding From The ReMap2022 Project

Usage

findSupportingRemapPeaks(results, genome, TFClass = FALSE)

Arguments

results	The output of motifbreakR
genome	Character; one of: hg38 or hg19 for Homo sapiens, mm10 or mm39 for Mus musculus, dm6 for Drosophila melanogaster, TAIR10_TF or TAIR10_HISTONE for Arabidopsis thaliana
TFClass	Logical; The user may optionally query an expanded motif/transcription factor relationship encompassing the entire potential transcription factor family as implemented by MotifDb based on TFClass.

Details

TFClass argument works for objects loaded in from the MotifDb package. hg19 and mm39 are data from liftOver.

The ReMap catalogues (2022, 2020, 2018, 2015) are under CC BY-NC 4.0 international license, as described in ReMap.

The CC BY-NC 4.0 license correspond to the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. NonCommercial — You may not use the material for commercial purposes. No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

Value

the results GenomicRanges object output by motifbreakR containing with the additional columns:

matchingBindingEvent	The name of the transcription factor that binds over the motif, or NA if none
matchingCellType	A list corresponding in length to the number of transcription factors in matchingBindingEvent indicating the biotype/celltype that the transcription factor binding was found in.

See Also

associateTranscriptionFactors for information about TFClass. https://remap.univ-amu.fr/ for details about ReMap2022.

Examples

data(example.results)

example.results <- findSupportingRemapPeaks(example.results,
                                            genome = "hg19",
                                            TFClass = TRUE)

Simon-Coetzee/motifBreakR documentation built on July 13, 2024, 7:12 p.m.