get_related_genes: Annotate peaks based on regions of peak

In jiang-junyao/IReNA: IReNA

Annotate peaks based on regions of peak

Description

This function first merge and extend footprint regions, and then integrate R package ChIPseeker to get footprint-related genes

Usage

get_related_genes(footprints, motif, Species, txdb, tssRegion = c(-3000, 3000))

Arguments

footprints	footprints that overlap with peaks, generated by overlap_footprints_peaks() or intersect function of bedtools
motif	motif file, you can choose our bulit-in motif database of 'mus musculus', 'homo sapiens', 'zebrafish' and 'chicken' by 'motif = Tranfac201803_Mm_MotifTFsF', 'motif = Tranfac201803_Hs_MotifTFsF', 'motif = Tranfac201803_Zf_MotifTFsF', 'motif = Tranfac201803_Ch_MotifTFsF' respectively, or you can upload your own motif data base, but the formata use be the same as our built-in motif database.
Species	character, indicating the species of data which is used to choose annodb when annotate peak.
txdb	TxDb object contained transcript-related features of a particular genome. Bioconductor provides several package that containing TxDb object of model organisms with multiple commonly used genome version, for instance TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene for human genome hg38 and hg19, TxDb.Mmusculus.UCSC.mm10.knownGene and TxDb.Mmusculus.UCSC.mm9.knownGene for mouse genome mm10 and mm9, etc.
tssRegion	Region Range of TSS

Value

return a list, first element is bed format datafrmae, second element is annotated footprints dataframe

Examples

#txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
load(system.file("extdata", "combined.rda", package = "IReNA"))
load(system.file("extdata", "test_peak.rda", package = "IReNA"))
peak_bed <- get_bed(test_peak)
overlapped <- overlap_footprints_peaks(combined, peak_bed)
#list1 <- get_related_genes(overlapped,txdb = txdb,motif=Tranfac201803_Mm_MotifTFsF,Species = 'Mm')

jiang-junyao/IReNA documentation built on Nov. 4, 2024, 8:29 p.m.