Problem with survival analysis with gene symbols containing hyphen
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0
Entering edit mode
21 days ago

Dear all,

I faced the problem of conducting a survival analysis with the gene symbols having hyphens, such as HLA-DPA1. I get the following error:

esca_HLA-DPA1= esca_matrix_vst %>% as.data.frame() %>% rownames_to_column (var='gene_id') %>% gather (key='case_id', value='counts', -gene_id) %>%
  left_join(. , gene_metadata, by="gene_id") %>%
  filter(gene_name == "HLA-DPA1")
Error in esca_HLA - DPA1 = esca_matrix_vst %>% as.data.frame() %>% rownames_to_column(var = "gene_id") %>%  : 
      object 'esca_HLA' not found

Can you advise me to change this code such that it can recognize the gene symbol?

Regards
Nazanin

R Survival-analysis • 258 views
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Entering edit mode
21 days ago
Darked89 4.6k

R dies not accept variable names with a dash in it. You should change esca_HLA-DPA1 to i.e esca_HLA_DPA1

See: https://www.w3schools.com/r/r_variables_name.asp

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Entering edit mode

Thank u so much for your comment. I will try it

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