pos2gff {ChIPseqR} | R Documentation

## Convert genome coordinates into GFF format

### Description

Provides facility to export the location of genomic features to a GFF formatted file.

### Usage

    pos2gff(pos, method, feature, len, strand, score, name)

### Arguments

`pos` | Named list with one component per chromosome giving the start position of features on that chromosome.
`method` | Entry for method field in GFF file. Recycled as necessary
`feature` | Entry for feature field in GFF file. Recycled as necessary
`len` | Length of fetures. This is used to calculate matching end positions for each start position given in `pos`
`strand` | Entry for feature field in GFF file. Recycled as necessary
`score` | Entry for feature field in GFF file. Recycled as necessary
`name` | Entry for feature field in GFF file. Recycled as necessary

### Value

A `data.frame` with columns `'chromosome'`, `'method'`, `'feature'`, `'start'`, `'end'`, `'score'`, `'strand'`. Writing this data frame to a text file produces a GFF formatted file.

### Author(s)

Peter Humburg

### References

The GFF specification: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml

### Examples

    pos <- list(chr1=c(10, 50, 60), chr2=c(22, 200, 500))
    pos2gff(pos, "test", "foo", 25, c("+", "+", "-", "+", "-", "-"), 0, "test")

[Package ChIPseqR version 1.46.0 Index]