getGeneSeq {ChIPpeakAnno} | R Documentation

## 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

### Note

internal function not intended to be called directly by users

### Author(s)

Lihua Julie Zhu

### 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)
    }

[Package ChIPpeakAnno version 3.12.7 Index]