dmgatti / doqtl Goto Github PK
View Code? Open in Web Editor NEWQTL mapping for Diversity Outbred mice (and other multi-founder advanced intercrosses)
QTL mapping for Diversity Outbred mice (and other multi-founder advanced intercrosses)
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$id
which I then use at the end of the function:
row.names(out) <- row.sdps
I changed the return() to out <- in three places to have out available.
Brian
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row.sdps <- sdps$id
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sdps = cbind(pos = sdps[,2], sdp = sdps[,ncol(sdps)], sdps[,-c(1:5,ncol(sdps))])
...
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row.sdps <- sdps$id
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sdps = cbind(pos = sdps[,2], sdp = sdps[,ncol(sdps)], sdps[,-c(1:5,ncol(sdps))])
...
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row.sdps <- sdps$id
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sdps = cbind(pos = sdps[,2], sdp = sdps[,ncol(sdps)], sdps[,-c(1:5,ncol(sdps))])
...
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return(data.frame(chr = rep(markers[1,2], length(stat)),
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sdp = sdps, LOD = stat))
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out <- data.frame(chr = rep(markers[1,2], length(stat)),
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sdp = sdps, LOD = stat)
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row.names(out) <- row.sdps
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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,
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:
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:
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!
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