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Old 04-19-2012, 02:26 PM   #21
Starr_Hazard
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Location: South Carolina

Join Date: Nov 2010
Posts: 19
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I am in a similar fix and I am a cummeRbund newbie too.

I am running R-2.15.2 and the BioConductor loaded cummeRbund so as of the first of the month I am mostly up-to-date.

What I want to do is to make a series of graphs from my significant isoform and splice sets.

getGene does not retrieve anything when given an isoform ID or splicing ID. I want to find the gene id corresponding to a given
isoform id or splice id

Per the Loyal's suggestion of the April 1 I can examine an isoform feature table eg:

sigIsoformFeatures
isoform_id gene_id CDS_id gene_short_name TSS_group_id class_code
657 TCONS_00000661 XLOC_000361 NA Syt5 TSS449 j
1651 TCONS_00001656 XLOC_000935 NA Grm5 TSS1161 =

Here's part of my sig isoform set:

head(mysigIsoforms,length(mysigIsoforms))
[1] "TCONS_00000661" "TCONS_00001656" "TCONS_00001659" "TCONS_00001672"

what's the syntax for getting the gene_id that matches the isoform id? For "TCONS_00000661" I want to select one of these "XLOC_000361" or "TSS449" or "Syt5"

The following loop work for plotting a set significant genes. It selects the ith geneID gets the gene and makes various plots. I'd like to use this if I can generalize it to examine the feature table.


Quote:
x<-length(Sham_vs_Expt.sigIsoforms)
x
print(x)


for(i in 1:x) {
print(Sham_vs_Expt.sigIsoforms[i])
myGeneID<-Sham_vs_Expt.sigIsoforms[i]
myGeneID
myGene<-getGene(cuff,myGeneID)
print(myGene)
head(fpkm(myGene))
head(fpkm(isoforms(myGene)))
gl<-expressionPlot(myGene)
print(gl)
gb<-expressionBarplot(myGene)
print(gb)
igb<-expressionBarplot(isoforms(myGene))
print(igb)

}
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