Replace XLOC id with gene symbol in FPKMmatrix function
I am using FPKM matrix function in cummeRbund as follows
gene.matrix<-fpkmMatrix(genes(cuff))
However, I am interested in plotting Ensembl ids or Gene symbols instead of XLOC ids. Is there a way to edit fpkm matrix function in order to use gene_short_name instead of gene_id?
Thanks
• 3,224 views
•
link
updated
by
Biostar
•
written
by
Satyajeet Khare
•
written
by
Satyajeet Khare
1 answer
Found one way.
gene.matrix<-fpkmMatrix(genes(cuff), fullnames=TRUE)
• 1 views
•
link
written
by
Satyajeet Khare
Log in to answer this question.
More posts like this
-
Genes' fpkm values through cufflink
written by arsala521 •
-
How to map old Ensembl Gene IDs to HGNC symbols and Entrez IDs
written by confused but trying •
-
Get gene names from ensembl ID or gene region
written by L. A. Liggett
-
Cuffdiff genes.fpkm_tracking xloc IDs to Ensembl IDs
written by bryce.kirby •
-
no XLOC gene_id or TCONS transcript_id in fpkm_tracking files
written by jolin0701-dy
-
Retrieve gene sets from Cuffdiff/Cuffnorm output with self defined criteria
written by Wet&DryImmunology
-
cummerbund cuffset filtering to subset or making a significance matrix from a cuffgeneset
written by dtmulder •
-
Gene_short_name missing in CuffDiff output (or how to retrieve it?)
written by nevev
-
Cummerbund Creating Gene Set
written by federico.gaiti
-
Cummerbund Gene Tracking
written by Eric •
