tGene {ballgown} | R Documentation |
Connect a transcript to its gene
Description
find the gene to which a transcript belongs
Usage
tGene(bg, transcript, tid = TRUE, gid = TRUE, warnme = TRUE)
Arguments
bg |
ballgown object
|
transcript |
transcript identifier
|
tid |
set to TRUE if transcript is a numeric transcript
identifier (i.e., t_id in expression tables), or FALSE if
transcript is a named identifie (e.g., TCONS_000001 or
similar.
|
gid |
if FALSE , return the gene *name* associated with
transcript in bg instead of the gene *id*, which is returned
by default. Take care to remember that not all ballgown objects include
gene *name* information. (They do all include gene IDs).
|
warnme |
if TRUE , and if gid is FALSE , print a
warning if no gene name is available for the transcript. This could either
mean the transcript didn't overlap an annotated gene, or that no gene names
were included when bg was created.
|
Examples
data(bg)
tGene(bg, 10)
tGene(bg, 'TCONS_00000010', tid=FALSE)
tGene(bg, 10, gid=FALSE) #empty: no gene names included in bg.
[Package
ballgown version 2.10.0
Index]