Describe the bug
When using subset_voom() to subset voom object by specified genes, IF the specified genes are formatted as factor, then the resulting gene filtering is done using the numeric indexing corresponding to the factor levels(admittedly this seems like a rare case).
Expected behavior
I think that the expected behavior likely should be to interpret factors as character string in this case. The function could check formatting for input genes and in the case of factors print an informative message and interpret as character. In the case that true numeric vector is inputted, then it seems reasonable for the behavior to be using this as an index on the gene matrix.
Describe the bug
When using subset_voom() to subset voom object by specified genes, IF the specified genes are formatted as factor, then the resulting gene filtering is done using the numeric indexing corresponding to the factor levels(admittedly this seems like a rare case).
Expected behavior
I think that the expected behavior likely should be to interpret factors as character string in this case. The function could check formatting for input genes and in the case of factors print an informative message and interpret as character. In the case that true numeric vector is inputted, then it seems reasonable for the behavior to be using this as an index on the gene matrix.