Question: Cummerbund Creating Gene Set
1
gravatar for federico.gaiti
5.9 years ago by
Brisbane
federico.gaiti70 wrote:

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

R cummerbund cufflinks • 4.6k views
ADD COMMENTlink modified 5.8 years ago by Christopher10 • written 5.9 years ago by federico.gaiti70
1
gravatar for Christopher
5.8 years ago by
Christopher10
Christopher10 wrote:

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

ADD COMMENTlink written 5.8 years ago by Christopher10
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