pos2gff: Convert genome coordinates into GFF format

In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

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")

ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.