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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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"rcmat = readSnpMatrix" issue #29

Open JImenaParedes opened 7 years ago

JImenaParedes commented 7 years ago

Ok, the first part of the script works perfectly, but when i get to this part, everything fails.

rcmat = readSnpMatrix(datafile) Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input In addition: Warning message: In file(file, "rt") : file("") only supports open = "w+" and open = "w+b": using the former Please, help!

veseshan commented 7 years ago

Seems like the file you have generated is empty. - "no lines available in input"

Venkat

JImenaParedes commented 7 years ago

Thank you, i already solved that problem, but now, i get this,

fit=emcncf(oo) Warning message: In max(mafR.clust[seg$chrom < nX], na.rm = T) : no non-missing arguments to max; returning -Inf

And i get an incomplete plot at the end. Could you please help me solve this?

veseshan commented 7 years ago

Seems like an issue with the data. What do you get when you use the command: summary(oo$out$mafR.clust)

JImenaParedes commented 7 years ago

I get this Min. 1st Qu. Median Mean 3rd Qu. Max. NA's NA NA NA NaN NA NA 5

veseshan commented 7 years ago

There appear to be some fundamental problems with your data. The information you provide is so minimal that is unhelpful. The methodology is developed for high throughput sequencing data - that is read depths are measured at several thousand loci and a significant number (at least few hundreds) are heterozygous. You may want to obtain summary statistics of input data to see if these conditions are met.

Venkat

JImenaParedes commented 7 years ago

Hello again, im trying to run the program with some a different data and i get this error:

xx = preProcSample(rcmat) Error in 1:nchr : result would be too long a vector In addition: Warning message: In max(mat$chrom) : no non-missing arguments to max; returning -Inf

Could you help me please?

veseshan commented 7 years ago

There is something wrong with the data file. Examine the Chromosome variable.

lferreiraMD commented 4 years ago

Just for anyone that found this page through Google as I have. I've just encountered the same error. It turned out that the samples I was analyzing were aligned with NovoAlign, which adds a ".fa" string to each seqname/chromosome name on each read in the BAM file. The package worked fine after I corrected for it.

clbenoit commented 4 years ago

Hi everyone,

I am getting the same error Error in 1:nchr : result would be too long a vector when using the preProcSample() function.

As an example I use the following matrix stored in the 'rcmat' object :

Chrom Pos NOR.DP NOR.RD TUM.DP TUM.RD 1 17 43044318 0 0 943 943 2 17 43044367 0 0 1151 1151 3 17 43044416 0 0 874 874 4 17 43044464 0 0 394 394 5 17 43044513 0 0 96 96 6 17 43044562 0 0 27 27 7 17 43044610 0 0 2 2 8 17 43044659 0 0 0 0 9 17 43044708 0 0 0 0 10 17 43044756 0 0 0 0

Then i am calling :

preProcSample(rcmat,ndepth=10, het.thresh=0.01, snp.nbhd=5, cval=25, deltaCN=0, gbuild="hg19", hetscale=TRUE, unmatched=TRUE, ndepthmax=10000)

Does everyone has an idea ?

Please find attached my rcmat matrix. Thank you so much for your help

Clément

rcmat_example.txt

read.table("rcmat_example.txt", header = TRUE, sep = ",")

clbenoit commented 4 years ago

PS : I noticed that it is working when using this second attached matrix.

If we subset it like that rcmat_good <- rcmat_good[1:x,]. It is working until x is greater than 122. Otherwise we have the same error again...

However the working rcmat has 131 rows, the not working one 249. I can't figure it out...

rcmat_example_notworking.txt rcmat_example_working.txt

I also tried the pileup argument mentioned here :

https://github.com/mskcc/facets/issues/47