nathanskene/one2one

This package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml

one2one's Issues

Issue with load.homologs()

In load.homologs(), the following line:

# The table is badly formatted, so drop rubbish
hom_vert = suppressWarnings(hom_vert[!is.na(as.numeric(hom_vert$`HomoloGene ID`)),])

Now removes all data from the downloaded file: "http://www.informatics.jax.org/downloads/reports/HOM_AllOrganism.rpt"

This was noted here: neurogenomics/MAGMA_Celltyping#42 . This is causing a runtime failure in MAGMA_celltyping

The issue is caused because the column HomoloGene ID no longer exists. The new column names are:

[1] "DB Class Key"                           "Common Organism Name"                  
 [3] "NCBI Taxon ID"                          "Symbol"                                
 [5] "EntrezGene ID"                          "Mouse MGI ID"                          
 [7] "HGNC ID"                                "OMIM Gene ID"                          
 [9] "Genetic Location"                       "Genomic Coordinates (mouse: , human: )"
[11] "Name"                                   "Synonyms"  

@NathanSkene can you confirm but perhaps there has just been a name change for this column? This nomenclature will need to be updated throughout the package. I will do this and push the change once you confirm.

Thanks!