Gavin Ha

Hi @d-henness You're correct - in the snakemake pipeline the `gender/sex` options are not currently being used and defaults to `male` which excludes chrX. I was in the middle of...

Hi @d88020 and @vleblanc , You're right that it is possible that TITAN is estimating zero tumor purity and that would potentially lead to NaN values. Hopefully, the optimal solution...

Hi Luca, Sorry for the inconvenience. I was an oversight on my part not to have put this directly into the R documentation. I will add these to the documentation....

Thanks @fpbarthel As I probably mentioned in this issue, earlier, the table of states went down with the original website. TitanCNA is usually run with `symmetric=TRUE` because it simplifies the...

Hi @sbamin If regions are first deleted and then genome doubled, then (hopefully) the prediction is copy neutral LOH (NLOH) or amplified LOH (ALOH). The tumor ploidy parameter represents, in...

Hi @lbeltrame Is this a selected solution made by `selectSolutions.R`? If so, then some changes in issue #61 might help. Is this a single run with ploidy initialized to 2?...

Thanks, @lbeltrame. I think the commits associated with #61 might help. Also, what value are you setting for `--alphaK` in `titanCNA.R`? For WES data, try using a value between 1000...

Hi @sahilseth Sorry, there must be a bug in the string notation after correction. If you look at the `Corrected_MinorCN`, it is still equal to 0 and `Corrected_MajorCN` is 2,...

Hi @peterpdu You might want to consider modifying the following lines to use the `mm` genome https://github.com/gavinha/TitanCNA/blob/c4f94ee10e74e83869c9585501a3dacfee3464cc/scripts/R_scripts/titanCNA.R#L184-L189 This is untested and may cause issues throughout the rest of the main...

Hi @udp3f Are you able to show a plot of one of the chromosomes so that we can see what might be happening. Thanks, Gavin