haichaowang

icon indicating a website link https://sites.google.com/view/wanghc icon indicating an email [email protected]

icon company University of Cambridge icon location Cambridge icon location PhD student and Bioinformatician at University of Cambridge

Results 4 comments of haichaowang

[BUG] Character List columns cause an error in join_overlap_left()

the same bug happened when the meta col is 'DNAStringSet' , would you mind adding support to this? Thank you ~

segments with deletions become 'red' colored

in the attached pdf above, the chr 6, 9, 10, 13 have those 'red' deletions, quite strange...

segments with deletions become 'red' colored

Thank you gavinha, for `--estimateSubclones TRUE`, I didn't find this option in the wiki page, would you mean `--estimateScPrevalence TRUE` instead? Best, Haichao

segments with deletions become 'red' colored

Thanks, by adding `--estimateScPrevalence TRUE` and `--scStates "c(1,3)"`, the color label now becomes normal. and it is true that the light green seg indicating subclonal CNVs. see attached: [rerun_SLX-18760_SXTHSH03.FS_1.sort_plots_genomeWide.pdf](https://github.com/broadinstitute/ichorCNA/files/5611214/rerun_SLX-18760_SXTHSH03.FS_1.sort_plots_genomeWide.pdf) **could...