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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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what is included in HMM_CNV_predictions.HMMi6.leiden.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_genes.dat? #577

Open rpeys opened 1 year ago

rpeys commented 1 year ago

I'm trying to understand the gene level outputs, which I think I can find in HMM_CNV_predictions.HMMi6.leiden.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_genes.dat. Specifically, I'm trying to understand which genes get included in this table. I see that many genes are included which are predicted to have state 3, i.e. copy number neutral. Why are these genes included in the output (and if some genes which are copy number neutral are included, why aren't all genes included?)? I even noticed that some of my control samples were returned in this table with predicted state 3 (but, not all control samples). What is the logic for which cells/samples are included, especially if they are not predicted to have a CNV?

Further, I'm having trouble finding sufficient documentation for how to interpret the output files in general, including definitions of the features in "Extracting HMM Features." Can you please point me to any further tutorials or documentation?

Thank you!!

RaghadShu commented 10 months ago

Hi! Not a developer but maybe this https://github.com/broadinstitute/infercnv/issues/208 can help you with the second question. Best, Raghad