Cummerbund Creating Gene Set

Question

[federico.gaiti]

Hi all,

I am using cummeRbund, an R visualization package for Cufflinks high-throughput sequencing data.

I want to create a gene sets to be able to analyse the differentially expressed genes I'm interested in. THis is what the manual suggests:

> data(sampleData)
> myGeneIds<-sampleIDs
> myGeneIds

 [1] "XLOC_001363" "XLOC_001297" "XLOC_001339" "XLOC_000132"
 [5] "XLOC_001265" "XLOC_000151" "XLOC_001359" "XLOC_000069"
 [9] "XLOC_000170" "XLOC_000105" "XLOC_001262" "XLOC_001348"
[13] "XLOC_001411" "XLOC_001369" "XLOC_000158" "XLOC_001370"
[17] "XLOC_001263" "XLOC_000115" "XLOC_000089" "XLOC_001240"

> myGenes<-getGenes(cuff,myGeneIds)

where sampleIDs is a vector of 'gene_id' or 'gene_short_name' values to identify the genes I wish to select.

I made a normal .txt file with my genes, which looks like this:

"XLOC_000012"
"XLOC_000033"
"XLOC_000071"
"XLOC_000080"
"XLOC_000081"
"XLOC_000102"
"XLOC_000105"
"XLOC_000113"
"XLOC_000156"
"XLOC_000191"
"XLOC_000212"
"XLOC_000229"
"XLOC_000230"
"XLOC_000241"
"XLOC_000242"
"XLOC_000293"
"XLOC_000294"
"XLOC_000328"
"XLOC_000356"
"XLOC_000398"
"XLOC_000417"
"XLOC_000434"
"XLOC_000442"
etc...

Then, in R, I run these commands:

myGeneIds<-read.table("my txt file")
myGenes<-getGenes(cuff,myGeneIds)
> myGenes
CuffGeneSet instance for  1  genes

and what I got is just the analysis of the first gene in the txt file. But I have 577 genes in the txt file.

How can I make the vector with my gene_id in order to make cummeRbund work correctly?

THanks for help Federico

Answer 1

[Christopher]

Hey Federico, I don't know if you got help with this problem already, but I just discovered your question, which helped me answer one of my own. To address your problem of getting only 1 gene in your analysis, I found that, rather than putting each gene name on a new line in the .txt file, putting them all on the same line allows cummeRbund to recognize all genes in my list: "XLOC_000012" "XLOC_000033" "XLOC_000071" "XLOC_000080" "XLOC_000081" "XLOC_000102" "XLOC_000105"...etc.

I don't know how easy that will be for you considering you have 577, but it's one way to do it. If you happen to find an easier way, please share!

Chris

[muthurikim]

Six years later, did the above with the quotes and still got CuffGeneSet instance for 1 genes Any other way to go about this?