CNAmat does not contain gene symbol when using genome = "hg20"

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
r
Domain
bioinformatics, data-visualization

Research direction

Reproduce the CNAmat output for human genes with genome="hg20" and compare it with the mm10 output, focusing on whether gene symbols are included. Then trace the heatmap plotting step and determine whether it can be skipped without changing the requested CNAmat result. Done means human CNAmat includes gene symbols consistently and heatmap generation can be omitted.

Written by the indexing model from the issue text.

Description

Hello,

Thank you for this nice package!

When I use human genes, the output CNAmat does not contain gene symbol. However, when I use genome="mm10", there is a column in CNAmat which stores gene symbol. Why they are different?

I noticed in the note Only difference is that the result is output in gene space instead of genomic space. Meaning the locations of CNVs is labelled by gene names, instead of genomic positions. . Can gene names be added to CNAmat output based on human genome?

Can the heatmap plotting step be omitted? It is time consuming.

Many thanks!

Dominant language
R
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