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Documentation Note 1 #36

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cassondranewman opened this issue Nov 9, 2023 · 1 comment
Open

Documentation Note 1 #36

cassondranewman opened this issue Nov 9, 2023 · 1 comment

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@cassondranewman
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cassondranewman commented Nov 9, 2023

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
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kose-y commented Nov 14, 2023

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

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