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dmgatti / DOQTL

QTL mapping for Diversity Outbred mice (and other multi-founder advanced intercrosses)
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Outdated URLs in calc.genoprob.R #7

Open penyuan opened 4 months ago

penyuan commented 4 months ago

Hello,

When using the function calc.genoprob(), it tries to retrieve data from ftp.jax.org, such as in lines 541-550 in calc.genoprob.R: 

  } else if(array == "gigamuga") {
    snpfile  = "ftp://ftp.jax.org/MUGA/GM_snps.Rdata"
    sexfile  = "ftp://ftp.jax.org/MUGA/GM_sex.Rdata"
    codefile = "ftp://ftp.jax.org/MUGA/GM_code.Rdata"
    xfile    = "ftp://ftp.jax.org/MUGA/GM_x.Rdata"
    yfile    = "ftp://ftp.jax.org/MUGA/GM_y.Rdata"
    genofile = "ftp://ftp.jax.org/MUGA/GM_geno.Rdata"
    if(sampletype == "HS") { 
      codefile = "ftp://ftp.jax.org/MUGA/GM_hs_code.Rdata"
    } # if(sampletype == "HS")

In this example, ftp://ftp.jax.org/MUGA/GM_snps.Rdata no longer resolves because the file GM_snps.Rdata no longer exists.

There is a README.txt in that path which points to:

https://www.jax.org/research-and-faculty/genetic-diversity-initiative/tools-data/diversity-outbred-reference-data

It's unclear how the data within GM_snps.Rdata was structured, so even if I download the newer data files at the URL above, I don't know how to make it work with DOQTL.

Can the developers @dmgatti, @dtenenba, @hpages, @mrjc42, @vobencha et al. please advise on how to fix this?

Thank you!

hpages commented 4 months ago

@penyuan Not sure why you are tagging me here. I don't remember being involved in the developement of the DOQTL package and I don't see my name in its DESCRIPTION file either. It seems that at some point the package was part of Bioconductor but it's been removed about 5 years ago (with BioC 3.10). So tagging the current maintainer (@dmgatti) should be enough. Thanks!

penyuan commented 4 months ago

Thank you for your response @hpages and the explanation. I wasn't sure who the main person is, so I tagged everyone listed as a "Contributor" to this repository. Sorry to bother you!