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OpenMendel / OrdinalGWAS.jl

Genome-wide association studies (GWAS) for ordered categorical phenotypes
https://openmendel.github.io/OrdinalGWAS.jl/latest/
MIT License
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Documentation Note 1 #36

Open cassondranewman opened 1 year ago

cassondranewman commented 1 year ago

Hello, Thank you for this FANTASTIC resource!!

I just wanted to make a note about a [potential ?] error I found in your documentation at https://openmendel.github.io/OrdinalGWAS.jl/stable/#Basic-usage

You give three lines of code to check that individual names match between phenotype and genotype files match - great idea. Your tutorial code: covdf = CSV.read(datadir "covariate.txt", DataFrame) plkfam = CSV.read(datadir "hapmap3.fam", header=0, delim=' ', DataFrame) all(covdf[!, 1] .== plkfam[!, 1]) && all(covdf[!, 2] .== plkfam[!, 2])

However fam files may be separated by tab delimeter, causing the statement to yeild FALSE. You may want to change your code accordingly to help users :) covdf = CSV.read(datadir "covariate.txt", DataFrame) plkfam = CSV.read(datadir "hapmap3.fam", header=0, delim='\t', DataFrame) all(covdf[!, 1] .== plkfam[!, 1]) && all(covdf[!, 2] .== plkfam[!, 2])

kose-y commented 12 months ago

Thanks for your notice. We will update our documentation soon.