seq2gene: seq2gene

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

seq2gene

Description

annotate genomic regions to genes in many-to-many mapping

Usage

seq2gene(seq, tssRegion, flankDistance, TxDb, sameStrand = FALSE)

Arguments

seq	genomic regions in GRanges object
tssRegion	TSS region
flankDistance	flanking search radius
TxDb	TranscriptDb object
sameStrand	logical whether find nearest/overlap gene in the same strand

Details

This funciton associates genomic regions with coding genes in a many-to-many mapping. It first maps genomic regions to host genes (either located in exon or intron), proximal genes (located in promoter regions) and flanking genes (located in upstream and downstream within user specify distance).

Value

gene vector

Author(s)

Guangchuang Yu

Examples

## Not run: 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
TxDb <- TxDb.Hsapiens.UCSC.hg19.knownGene
file <- getSampleFiles()[[1]] # a bed file
gr <- readPeakFile(file)
genes <- seq2gene(gr, tssRegion=c(-1000, 1000), flankDistance = 3000, TxDb) 

## End(Not run)

YuLab-SMU/ChIPseeker documentation built on Nov. 2, 2024, 1:45 p.m.