Z States output

[aelhossiny]

Hi, I am trying to compare events in clones from different samples to determine if I can define conserved events in certain cancer. As an oncoprint and visual inspection of the events aren't efficient approaches, I wanted to select a sample-invariant metric I can use to cluster cells/pseudobulk-clones

In the paper, Supp Fig 6, you mentioned that "Hidden states in the Numbat joint HMM and their respective parameter configurations are marked in black solid dots. Each dashed line represents the possible expression change and allele fraction for a given genotype depending on the cell fraction and haplotype state (major or minor)."

Is this emitted as one of the analysis output? and can I use it to compare/clusters cells from different samples? If not, can I use the estimated phi phi_mle as a measure for copy number ratio to the diploid state?

Thanks

[teng-gao]

Hello,

The schematic in Supp Fig 6 only applies to pseudobulk CNV calling via HMM. Both phi_mle and theta_mle are outputted in segs_consensus. You can check the variable descriptions for output files here:
https://kharchenkolab.github.io/numbat/articles/descriptions.html