Error when following Example Usage

[AgentKumara]

Hi,

I was trying out this package, and came across what appears to be an error while running the Example Usage (using the example data).

> trainData = UCEC_mafs[UCEC_mafs$Tumor_Sample_Barcode %in% as.character(SampleID_train),]
> trainset = readData(trainData, exomef, covarf, mutContextf, ref)
Number of inconsistant annotation mutation: 0 out of total 0 mutation 
Bed file is not specified for samples. exomeGene for whole exome will be generated.
Total gene analyzed: 0

And then subsequently get this message:

> sample = data.frame(SampleID = SampleID_test, BED = TST170_panel, stringsAsFactors = FALSE)
> testData = UCEC_mafs[UCEC_mafs$Tumor_Sample_Barcode %in% as.character(SampleID_test),]
> testset_panel = readData(testData, exomef, covarf, mutContextf, ref, samplef = sample)
Number of inconsistant annotation mutation: 0 out of total 0 mutation 
Total 0 out of 176 samples with at least one mutation detected.
Only the ones with at least one mutation will be used.
Bed file is specified for samples
    All samples have the same bed regions
Error in `$<-.data.frame`(`*tmp*`, "Chromosome", value = "chr") : 
  replacement has 1 row, data has 0

Any idea what might be going on?

Thanks :)

[lijingya]

Hi It turns out the code was updated however the example data was little bit outdated. I made a change to fix this problem. You can pull the latest master branch.

Thanks

[AgentKumara]

Thanks! This seems to have fixed it :)