globals.R

# ---- globals ---- 
# Customize as needed for file locations

# Modify data.dir to indicate the location of the GWAStutorial files
# Intermediate data files will also be stored in this same location unless you set out.dir

# Intermediate data files will also be stored in this same location unless you set out.dir
data.dir <- '/scratch/spectre/a/asna4/GWAS'
out.dir <- '/scratch/spectre/a/asna4/GWAS/out'

gwas.fn <- lapply( c (bed='bed', bim='bim', fam='fam' ,gds='gds'), function (n) sprintf ("%s/GWAStutorial.%s", data.dir, n))
clinical.fn <- sprintf("%s/GWAStutorial_clinical.csv", data.dir)
onethou.fn = lapply(c(info='info' ,ped='ped'), function(n) sprintf("%s/chr16_1000g_CEU.%s", data.dir, n))
protein.coding.coords.fname <- sprintf ("%s/ProCodgene_coords.csv", data.dir)

# Output files
gwaa.fname <- sprintf ("%s/GWAStutorialout.txt ", out.dir)
gwaa.unadj.fname <- sprintf ("%s/GWAStutorialoutUnadj.txt", out.dir)
impute.out.fname <- sprintf ("%s/GWAStutorial_imputationOut.csv", out.dir)
CETP.fname <- sprintf("%s/CETP_GWASout.csv" , out.dir)

#saving configs
working.data.fname <- function(num) { sprintf("%s/working.%s.Rdata", out.dir, num) }