pos2gff {ChIPseqR} | R Documentation |
Provides facility to export the location of genomic features to a GFF formatted file.
pos2gff(pos, method, feature, len, strand, score, name)
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 |
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 |
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.
Peter Humburg
The GFF specification: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
pos <- list(chr1=c(10, 50, 60), chr2=c(22, 200, 500)) pos2gff(pos, "test", "foo", 25, c("+", "+", "-", "+", "-", "-"), 0, "test")