Post date: Sep 26, 2017 3:37:27 PM
26ix17.
I messed up back in June -- the subgroup-level breeding value correlation heat maps were made with the data from the "all" analysis, not from each "subgroup" analysis. So, I've deleted the code I used to make this incorrect heat maps, as well as the maps themselves, to avoid any confusion.
I will get help with writing a perl script to make the infiles for each subgroup and population, since there are a different number of individuals with measurements for size vs. position. There are 69 variables for everybody.
The modularity results are still correct, since I did size and position separately and use the raw bv_*.txt files.
18x17.
Ok, the group combined bv files are in /uufs/chpc.utah.edu/common/home/u6000989/projects/lycaeides_wings/Gemma/output_grps
ad are called catbv_*.csv where * = group. They should be in the same format as the example, except they lack the header row. The total numbers of individuals seem right, so I think they are in good shape.
The population ones are here:
/uufs/chpc.utah.edu/common/home/u6000989/projects/lycaeides_wings/Gemma/output_pops
and called catbv_*csv as well. I think these are all set too.
I used the catbv files to make the breeding value heat maps. SN stands out the most as different. See geno-heatmap.R for R code. pdfs are in dropbox and drive.