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

Run this code


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)
}

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