readRefmap: reads output in .refmap format from cuffcompare
In psikon/cuffgo: cufflinks and GO analysis

Description Usage Arguments Format Value References

This function reads output from the cuffcompare specific refmap format. It is an tab delimited file that lists, for each reference transcript, which cufflinks transcript either fully or partially match.

1	readRefmap(filename)

filename

location of the cuffcompare output file in .refmap format

Tab delimited file, where one row represents a reference transcript with the following attributes:

ref_gene_id: The gene_name attribute of the reference GTF record for this transcript, if present. Otherwise gene_id is used.
ref_id: The transcript_id attribute of the reference GTF record for this transcript
class_code: The type of match between the Cufflinks transcripts and the reference transcript.
cuff_id_list: A comma separated list of Cufflinks transcript ids matching the reference transcript