error while processing mouse data

[kvshams]

getting zero gene ortholog

ctd2 = prepare.quantile.groups(ctd,specificity_species = "mouse",
                               gwas_species = "human", numberOfBins=40)

[1] "Dropping all genes that do not have 1:1 homologs between the two species"
[1] "Species for which homology classes are available:"
character(0)
[1] "Available species options:"
[1] all    simple
<0 rows> (or 0-length row.names)
Error in check.species(requestedSpecies = species1, allSpecies = allHomologs$`Common Organism Name`): ERROR: species does not match available options
Traceback:

1. prepare.quantile.groups(ctd, specificity_species = "mouse", gwas_species = "human", 
 .     numberOfBins = 40)
2. One2One::analyse.orthology(specificity_species, gwas_species, 
 .     allHomologs)   # at line 7 of file <text>
3. check.species(requestedSpecies = species1, allSpecies = allHomologs$`Common Organism Name`)
4. stop("ERROR: species does not match available options")
5. 

While checking the code, it may be associated with One2One packages load.homologs.r

    hom_vert = read.table("http://www.informatics.jax.org/downloads/reports/HOM_AllOrganism.rpt",sep="\t",stringsAsFactors = FALSE,quote="") ```

 as the column header has been changed. Not sure what was the previous and how that column handled for the downstream for debugging.

[Al-Murphy]

Hi @kvshams,

Thanks for letting us know, I am able to replicate the error and am looking into a fix now. I'll update when it is resolved.

Kind regards,
Alan.

[kvshams]

@Al-Murphy Thanks.... it worked out well with just fixing the column name and it worked well. I included those changes in the pull at One2One.

[Al-Murphy]

Thanks @kvshams, we are investigating to see if the data has changed along with the column header, it appears there is a significant difference in the new dataset size. If you're interested, see the issue here:

NathanSkene/One2One#3

[Al-Murphy]

This issue has been resolved thanks to a fix to the OnetoOne package. @bschilder can you confirm if you plan to replace the use of OnetoOne down the line in your MAGMA_celltyping branch? @NathanSkene mentioned you might?

[bschilder]

@Al-Murphy sorry for the late reply, these were all getting sent to my spam folder.

Yes, I am planning on updating prepare.quantile.groups() to take advantage of the upgrades in interspecies gene conversion in the DelayedArray branch of EWCE