Copy Number Variations (CNV) gene_pos_df

theMILOlab / SPATA2

A Toolbox for Spatial Transcriptomics Analysis

https://themilolab.github.io/SPATA2/

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Copy Number Variations (CNV) gene_pos_df #8

Closed hzongyao closed 2 years ago

hzongyao commented 3 years ago

hi I found the outcome related gene_pos_df of Running CNV-Analysis is strange, Why some genes are located on chr 0，like ASAP3，Just like the website example, why do chr0, chr23, chr24 appear？ https://themilolab.github.io/SPATA2/articles/spata-v2-cnv-analysis.html

Thank you ！

hzongyao commented 3 years ago

I have read related code about how gene_pos_df is created, I hope the end outcome can exclude chr0,Thank you!

kueckelj commented 3 years ago

Hello hzongyao,

the data.frame gene_pos_df is created by the function CONICSmat::getGenePositions(). Code Line 415. If you are not satisfied with the way this function outputs the gene position data.frame:

I have updated the function runCnvAnalysis(). Using the argument gene_pos_df you can provide the data.frame the way you want it. This way you should be able to exclude chromosomes that you do not want to be part of the analysis.

Does this solve the problem?