bioinform / ectmb Goto Github PK

Dear sir,
I cannot find a way to put my own data in the TMB model.
Is the input a maf file from Mutect2?
Do you have any suggestion?

Dear developer, thank you for your great effort. I'm facing a problem that I'm not able to find a solution. How is it possible that when I apply your algorithm to my own data I found a TMB's value higher (for example 200 vs 10) in total WES than in panel? (COnsidering that the experiment is made with Agilent Panel, so the entire WES is not full sequenced?)

Hello everyone,

this is not an issue, but rather I wanted to share the recipe I have written to wrap the ecTMB library in a Singularity container.

Any questions, feel free to ask.

Regards

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 :)

Hello,

I found a bug in the fit_model function, which only reveals itself if one tries to use some other name for the trainset variable.

Here:

It will be great if you fix it in the next release!

Best wishes,
Aleksandra

Hi!

I found a bug in procMaf.R line 253 (maf_dnp_converter function):

With my dataset, I got an error while performing readData, which traced back to this bug.

> trainset       = readData(trainData, exomef, covarf, mutContextf, ref)
Error in matrix(0, nrow = nrow(mutab.onp) * umaxchar[k], ncol = ncol(mutab.onp)) : 
  invalid 'nrow' value (too large or NA)

It appears that within the loop, the mutab.onp variable sometimes only contains one row, which means that it is treated as a vector and hence nrow(mutab.onp) returns NULL. It looks like the previous line, 252, was supposed to correct that, but it is formulated very strangely - length(mutab.onp) will depend on the number of accessory columns and will not necessarily be 8 when there is one row only. A fix along the lines of

if ( is.null(nrow(mutab.onp) ){mutab.onp = t(as.matrix(mutab.onp))}

is suggested.

Best regards,
Aleksandra

Hello,

I am having difficulty to run this program, will it work with hg18/GRCh37?

Thank you