ChIPpeakAnno (version 3.6.5)

getGeneSeq: Get gene sequence using the biomaRt package

Description

Get gene sequence using the biomaRt package

Usage

getGeneSeq(LocationParameters, mart)

Arguments

LocationParameters

c(ensembl_gene_id, distance from the peak to the transcription start site of the gene with the above ensemblID, upstream offset from the peak, downstream offset from the peak, Gene Start, Gene End)

mart

see useMart of bioMaRt package for details

Value

a list with the following items

feature_id

ensemble gene ID

distancetoFeature

distance from the peak to the transcriptionstart site of the gene with the above ensembl gene ID

upstream

upstream offset from the peakStart

downstream

downstream offset from the peakEnd

seq

sequence obtained around the peak with above upstream and downstream offset

Examples

if (interactive())
{
mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
LocationParameters =c("ENSDARG00000054562",400, 750, 750,40454140,40454935)
getGeneSeq(LocationParameters, mart)

LocationParameters =c("ENSDARG00000054562",752, 750, 750,40454140,40454935)
getGeneSeq(LocationParameters, mart)
 
LocationParameters =c("ENSDARG00000054562",750, 750, 750,40454140,40454935)
getGeneSeq(LocationParameters, mart)
 
 LocationParameters =c("ENSDARG00000054562",-2, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart)

 LocationParameters =c("ENSDARG00000054562",0, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart)
 
 LocationParameters =c("ENSDARG00000054562",2, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart) 
 
 LocationParameters =c("ENSDARG00000054562",1000, 750, 750,40454140,40454935)
 getGeneSeq(LocationParameters, mart)
}