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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Subsequent runs of the HMM #458

Open hahia opened 2 years ago

hahia commented 2 years ago

Can I first run infercnv::run with HMM=False and then run HMM with the output of infercnv::run(HMM=False)? I don't want to re-run infercnv::run(HMM=True). it will take a lot of time.

GeorgescuC commented 2 years ago

Hi @hahia ,

If you want to run the HMM, there is an extra step to generate the hidden spike data that is done early on and following steps are applied to that data as well, so if you have HMM=FALSE on a run, this is data is not generated and most steps will need to be rerun to enable the HMM. What you can however do is to call run(HMM=TRUE, up_to_step=16) so that the steps required by the HMM are run, but the HMM itself is not as it starts at step 17. This allows you to later simply remove the up_to_step argument so that the HMM is run without having to rerun the earlier steps.

Regards, Christophe.