Closed liannesuurenbroek closed 1 year ago
Hi @liannesuurenbroek,
Both tmp[,2]
and tmp[,3]
should be integers, not letters. I don't know if the documentation clearly explains what the allele files should contain, apologies for any confusion. I'll check and add a short description. It should be integers and follows the order of the output from alleleCounter: A, C, G and T. As an example, here is the very beginning of our reference file for WES (chr 1; tab-separated):
position a0 a1 10642 3 1 11008 2 3 11012 2 3
This means that chr1:10642 is a G>A SNP and both chr1:11008 and chr1:11012 are C>G SNPs.
You can easily convert letters to integers using: c('A'=1,'C'=2,'G'=3,'T'=4)[tmp[,2]]
(please check that tmp[,2]
only contains A/C/G/T). Hope this helps, let me know if something is still unclear.
Cheers,
Tom.
Hi,
I was indeed wondering about that, but I couldn't find which integer corresponds to which nucleotide so I assumed I could also fill in the letters. Thanks for the explanation!
Hi @liannesuurenbroek,
No problem, I've updated the doc (https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WES#file-format) so it's now described.
Cheers,
Tom.
Hi, I got the following error when using ascat.prepareHTS using my own alleles and loci data:
I think I found the source of the error in line 334 of the readAllelesFiles function in ASCAT/R/ascat.prepareHTS.R:
tmp=tmp[!is.na(tmp[,2] & !is.na(tmp[,3])),]
Since tmp[,2] is a letter in my case (instead of a number in the standard allele files), this line throws an error. I think the code should instead say:tmp=tmp[!is.na(tmp[,2]) & !is.na(tmp[,3]),]
Is this correct? Thanks!