Dan,
I made the following changes to assoc.scan1 on my local copy. I could not make changes to your github of course. These allow sanger ID to be row names of return data frame, helping user identify key SNPs. Below is diff part. That is, around line 427 of assoc.map.R I added
row.sdps <- sdps$id
which I then use at the end of the function:
row.names(out) <- row.sdps
I changed the return() to out <- in three places to have out available.
Brian

426
426

Convert the DO haplotype probabilities to Sanger alleles.

427

Kludge: Preserve Sanger ID for output.

428
row.sdps <- sdps$id
427
429
sdps = cbind(pos = sdps[,2], sdp = sdps[,ncol(sdps)], sdps[,-c(1:5,ncol(sdps))])
...
426
426

Convert the DO haplotype probabilities to Sanger alleles.

427

Kludge: Preserve Sanger ID for output.

428
row.sdps <- sdps$id
427
429
sdps = cbind(pos = sdps[,2], sdp = sdps[,ncol(sdps)], sdps[,-c(1:5,ncol(sdps))])
...
426
426

Convert the DO haplotype probabilities to Sanger alleles.

427

Kludge: Preserve Sanger ID for output.

428
row.sdps <- sdps$id
427
429
sdps = cbind(pos = sdps[,2], sdp = sdps[,ncol(sdps)], sdps[,-c(1:5,ncol(sdps))])
...
483

return(data.frame(chr = rep(markers[1,2], length(stat)), 

484

       sdp = sdps, LOD = stat))

485
out <- data.frame(chr = rep(markers[1,2], length(stat)),

486
sdp = sdps, LOD = stat)

487

489

Kludge to get row names, which are SNPs.

490
row.names(out) <- row.sdps

491
out

Hello,

I am having a warning and I don't know if that are altering the results I am having

I am running this function:

assoc.map(
pheno = pheno,
pheno.col = c(5),
probs = model.probs6,
K = K3,
addcovar = covar,
snps = muga_snps,
chr = 15,

chr = interval[1, 2], # here you can call values in interval

start = interval[1, 3],

end = interval[3, 3]

start = 74.000, # or you can insert only the values here
end = 78.000 # ideally these regions are the regions where the QTLS are located
)

This generates this warning:

Warning message:

In .vcf_map_samples(samples(hdr), samples) : samples not in file: ‘C57BL_6J’

Do you know what does it means?

Thanks a lot.

The session info is:
sessioninfo_020920.txt

Hi Dan,

Small bug in DOQTL. If you have only one sex (‘males’ in my case), the effect plot for chrX does not work.

  download.file("http://dl.dropboxusercontent.com/u/232839/class_k__Bacteria.Other.Other.rds", "temp.rds")
  fit <- readRDS("temp.rds")
  coefplot(fit, chr = "X", sex="M")

I am getting an error

Error in `colnames<-`(`*tmp*`, value = `*vtmp*`) : 
  attempt to set 'colnames' on an object with less than two dimensions

My guess is you need to add “drop==FALSE” somewhere in you code :-)

In the rankZ function located in the rankZ.R script, the denominator is written as "(sum(!is.na(x)) + 1)". Should this be corrected to subtract 1?

Thank you.

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!