search

wenweixiong / MARVEL

38 stars 9 forks source link

AnnotateGenes.10x not annotating 'gene_type' #6

Closed jesswhitts closed 1 year ago

jesswhitts commented 1 year ago

Hello,

First of all, thanks for the great tool!

I am following the 10X tutorial you have posted. When running the function AnnotateGenes.10x, the gene_type annotations are not maintained, and are just listed as:

table(marvel$gene.metadata$gene_type) character(0) 17533

Strangely though when I copy the code from "Script_DROPLET_02_PREPROCESS_1_AnnotateGenes.R", it runs perfectly fine:

table(marvel$gene.metadata$gene_type) IG_C_gene IG_C_pseudogene IG_V_pseudogene lncRNA protein_coding TR_C_gene TR_V_gene 1 1 1 3666 13855 6 3

I have tried re-installing the package and it has made no difference. Unsure what the issue is, or if there even is an issue, just something to be aware of :)

Best, Jess

wenweixiong commented 1 year ago

Hi Jess,

Thank you for reaching out :)

This issue has been fixed since version 2.0.1.

Please may you re-install the package from Github (not CRAN)?

library(devtools) install_github("wenweixiong/MARVEL") library(MARVEL)

Sean

jesswhitts commented 1 year ago

ah, sorted now. Thanks!