I am having an issue with gene tracking in cummeRbund. Here is the cuff output:
> cuff CuffSet instance with: 4 samples 23285 genes 30073 isoforms 25872 TSS 24748 CDS 139440 promoters 155232 splicing 122340 relCDS
But when I try to run gene tracking, the following happens:
> myGeneId <- "ENSMUSG00000045440" > myGene <- getGene(cuff,myGeneId) > myGene CuffGene instance for gene ENSMUSG00000045440 Short name: ENSMUSG00000045440 Slots: annotation features fpkm repFpkm diff count isoforms CuffFeature instance of size 1 TSS CuffFeature instance of size 0 CDS CuffFeature instance of size 0 > genetrack <- makeGeneRegionTrack(myGene) Error in `[.data.frame`(features(object), , featCols) : undefined columns selected
Therefore, I'm unable to visualize transcript-level features of my gene of interest. I am using an Ensembl gtf and have set
but no luck. I have also tried using the cummeRbund cufflinks data from the sample directory
but still no luck. I have no issue analyzing 'myGene' or any other cummeRbund feature, so I assume I've accessed the data correctly. Any ideas on what the problem might be?