hello, as some of you have noticed, there are a few (mostly minor) code problems with the tutorial. One is in the data pre-processing section, after the pca plot, please COMMENT OUT:
closefn.gds(genofile)
Another is in the command
thougeno <- read.pedfile(onethou.fn$ped, snps = onethou.fn$info, which=1)
You will probably need to change the file names:
thougeno <- read.pedfile(chr16_1000g_CEU.ped, snps = chr16_1000g_CEU.info, which=1)
Also, in the Post-analytic and genomic visualization section, COMMENT OUT:
llplusgenes <- LDheatmap.addGenes(ll, chr = "chr16", genome = "hg19", genesLocation = 0.01)
and see how it goes from there (you will have to change the variable names to remove llplusgenes.
Lastly, you do NOT have to do the Regional Association section at the very end.
Please let me know if you have any questions,
Best regards,
Darlene
