How to sort out error in gdcCEAnalysis function of GDCRNATools R package?
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0
Entering edit mode
Bhavya • 0
@d707106c
Last seen 7 weeks ago
India

I want to use the GDCRNATools R package. I am trying to use its gdcCEAnalysis function. In the example of this function, the following code is mentioned.

library(GDCRNATools)
 deLNC <- c('ENSG00000260920','ENSG00000242125','ENSG00000261211')
 dePC <- c('ENSG00000043355','ENSG00000109586','ENSG00000144355')
 genes <- c(deLNC, dePC)
 samples <- c('TCGA-2F-A9KO-01', 'TCGA-2F-A9KP-01', 
             'TCGA-2F-A9KQ-01', 'TCGA-2F-A9KR-01', 
             'TCGA-2F-A9KT-01', 'TCGA-2F-A9KW-01')
 rnaExpr <- data.frame(matrix(c(2.7,7.0,4.9,6.9,4.6,2.5,
                     0.5,2.5,5.7,6.5,4.9,3.8,
                     2.1,2.9,5.9,5.7,4.5,3.5,
                     2.7,5.9,4.5,5.8,5.2,3.0,
                     2.5,2.2,5.3,4.4,4.4,2.9,
                     2.4,3.8,6.2,3.8,3.8,4.2),6,6), 
                     stringsAsFactors=FALSE)
 rownames(rnaExpr) <- genes
 colnames(rnaExpr) <- samples

 mirExpr <- data.frame(matrix(c(7.7,7.4,7.9,8.9,8.6,9.5,
                     5.1,4.4,5.5,8.5,4.4,3.5,
                     4.9,5.5,6.9,6.1,5.5,4.1,
                     12.4,13.5,15.1,15.4,13.0,12.8,
                     2.5,2.2,5.3,4.4,4.4,2.9,
                     2.4,2.7,6.2,1.5,4.4,4.2),6,6),
                     stringsAsFactors=FALSE)
 colnames(mirExpr) <- samples
 rownames(mirExpr) <- c('hsa-miR-340-5p','hsa-miR-181b-5p',
                     'hsa-miR-181a-5p', 'hsa-miR-181c-5p',
                     'hsa-miR-199b-5p','hsa-miR-182-5p')

 ceOutput <- gdcCEAnalysis(lnc       = deLNC, 
                         pc          = dePC, 
                         lnc.targets = 'starBase', 
                         pc.targets  = 'starBase', 
                         rna.expr    = rnaExpr, 
                         mir.expr    = mirExpr)

The above mentioned code gives the following output:

Step 1/3: Hypergenometric test done !
Step 2/3: Correlation analysis done !
Step 3/3: Regulation pattern analysis done !

However, if the values in deLNC are changed, the gdcCEAnalys function shows the following error:

deLNC <- c('ENSG00000000003','ENSG00000099869','ENSG00000261211')
#rest of the code is same.

Error in `colnames<-`(`*tmp*`, value = c("lncRNAs", "Genes", "Counts",  : 
  attempt to set 'colnames' on an object with less than two dimensions

Please help me in understanding the cause of this error. The details of the package and function can be found here: https://rdrr.io/bioc/GDCRNATools/src/R/gdcCEAnalysis.R https://rdrr.io/bioc/GDCRNATools/man/gdcCEAnalysis.html

GDCRNATools • 133 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 17 hours ago
United States

If I understand the function correctly, the deLNC object is supposed to contain lncRNA IDs, right? And if you put regular gene IDs like ENSG00000000003 that probably doesn't work correctly. Ideally it would filter out non-lncRNA IDs, I suppose, but ideally the end users wouldn't be passing in regular gene IDs as lncRNAs.

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