convert_orthologs() output is list, with "Warning: Coercing LHS to a list" about orthogene HOT 5 CLOSED

Ok, so the issue was that internally orthogene was converting the single-column data.frame (your input) to a vector, which is the default behaviour of R.

orthogene/R/filter_gene_df.R

Line 15 in 146f54e

gene_df2 <- gene_df[genes %in% gene_map$input_gene, ]

I've edited the code above to avoid this. Will push the changes to the Bioc release with this fix, but in the meantime the easier solution for you would be to add a dummy column to your input data.frame, which will prevent it from getting turned into a vector later on.

human_genes <- data.frame(read.csv("Human_gene_list_reprex.csv"))
human_genes$dummy <- NA

Let me know if that works for you!

This worked! Thanks so much!

from orthogene.

Thanks for the detailed reprex @ehickman0817! Though I can't seem to find the "Human_gene_list_reprex.csv" file you mentioned.

from orthogene.

Thanks for the detailed reprex @ehickman0817! Though I can't seem to find the "Human_gene_list_reprex.csv" file you mentioned.

Ah, actually found it in the SessionInfo!
https://github.com/neurogenomics/orthogene/files/12004790/Human_gene_list_reprex.csv

from orthogene.

Thanks for the detailed reprex @ehickman0817! Though I can't seem to find the "Human_gene_list_reprex.csv" file you mentioned.

Ah, actually found it in the SessionInfo! https://github.com/neurogenomics/orthogene/files/12004790/Human_gene_list_reprex.csv

Great, thanks! Sorry, this is my first time posting a reprex, glad you found it!!

from orthogene.

Ok, so the issue was that internally orthogene was converting the single-column data.frame (your input) to a vector, which is the default behaviour of R.

I've edited the code above to avoid this. Will push the changes to the Bioc release with this fix, but in the meantime the easier solution for you would be to add a dummy column to your input data.frame, which will prevent it from getting turned into a vector later on.

human_genes <- data.frame(read.csv("Human_gene_list_reprex.csv"))
human_genes$dummy <- NA

Let me know if that works for you!

from orthogene.