InferCNV score visualisation

[Amin Ali]

Hi there,

I was wondering if anybody can suggest a way to visual inferCNV score in R to differentiate normal vs tumour? Is it also possible to not only get a box/violin plot, but also projecting the score on the UMAP like on infercnvpy (https://icbi-lab.github.io/infercnvpy/tutorials/tutorial_3k.html)

Thanks,

Amin

[cgeo...@broadinstitute.org]

Hi Amin,

You can project HMM predictions on the UMAP following this guide: https://github.com/broadinstitute/infercnv/wiki/Extracting-features

Regards,

Christophe.

[Amin Ali]

Thanks, Christophe for the link.

I'm getting an error:

WARN [2022-02-24 11:02:34] ::Could not find any HMM predictions outputs at: /mnt/gpfs2/data/poncol/aali/scRNA_files/Subclusters_LouvainClustering/InferCNV_Testing/InferCNV_objects

I have set the output to my inferCNV object folder as its path.

The version I'm using is 1.8.1.

Thanks,

Amin