nathanskene / one2one Goto Github PK
View Code? Open in Web Editor NEWThis package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml
This package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml
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!
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