Making Regional Association Plots with the gap package for R

Question

[Tobias.Wohland]

Hi guys,

I have a question regarding the gap package for R. I want to create regional association plots but I'm wondering where I can get the "THETA" which is needed for the map-argument. What exactly is it? Also "DIST" is not perfectly clear. Is it the distance to the leading SNP or the distance to a gene nearby or what exactly do they mean with it. It would be nice to have access to the example data of the package. Is it possible to get the CDNK-data of this package? I used goolge but couldn't find anything. It would be nice if someone could help me.

Sorry for those stupid questions but I'm not 100% familar with all this stuff.

Thanks in advance.

Best,

Tobi

[Jimbou]

Check the documentation of the function for some help:

?asplot()
asplot(CDKNlocus, CDKNmap, CDKNgenes)
head(CDKNlocus)
head(CDKNmap)
head(CDKNgenes)
haldane <- function(x) 0.5*(1-exp(-2*x))
locus <- with(info, data.frame(CHR=chr,POS=chrpos,NAME=marker,
                    DIST=(chrpos-min(chrpos))/1000000,
                    THETA=haldane((chrpos-min(chrpos))/100000000)))

I'm not sure what theta exactly means, but perhaps you can use the pipeline for your data, regardless the meaning. Could be some info for the recombination rate? Another possibility is the qqman package. Here is a nice tutorial. Subsequently you can use locuszoom for the regional plot.