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Modular reporting of output components & Conversion to S4 classes #43

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Modular reporting of output components & Conversion to S4 classes #43

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92 changes: 36 additions & 56 deletions R/analyze.R
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Original file line number Diff line number Diff line change
Expand Up @@ -33,65 +33,45 @@



analyze <- function(i = double(), j = double(), mode = "default", path.base = "/scratch/hpc2862/CAMH/perm_container/container_", summary.file = "/scratch/hpc2862/CAMH/perm_container/snp_summary2.out", output = "~/repos/coR-ge/data/test_run2.txt", test = TRUE, safe = TRUE, local = FALSE, h2 = 0.45, pc = 0.5, pnc = 0.5, nc = 1000, gen = NULL, summary = summary, maf = FALSE, maf_range = NULL){


#message(paste0("coR-ge v", packageVersion("coRge"), " \t \t http://github.io/Chris1221/coR-ge \n \n \t Parameters in use: \n \t \t i: ",i, "\n \t \t j: ", j, "\n \t \t path.base: ", path.base,"\n \t \t summary.file: ", summary.file,"\n \t \t output: ", output,"\n \t \t th2: ", h2,"\n \t \t pc: ", pc,"\n \t \t pnc: ", pnc,"\n \t \t nc: ", nc, "\n \n \t Local options: \n \t \t local: ", local,"\n \t \t gen ", gen,"\n \t \t summary: ", summary, " \n \n \t Testing options: \n \t \t test: ", test,"\n \t \t safe: ", safe, "\n \n LOG: \n"))



if(local) {

gen <- gen
summary <- summary

} else if(!local){

message("Error Checking")

if(any(is.null(c(i,j,path.base, summary.file)))) stop("Please complete all input arguemnets")

path <- paste0(path.base,i,"_",j,"/")
setwd(path)


message("Deleting junk files...")

list.files(path)[!grepl("controls.gen", list.files(path))] %>%
file.remove

message("Reading in genotype files...")

if(!test){

for(k in 1:5){
if(k == 1){
fread(paste0(path, "chr1_block_", i, "_perm_", j, "_k_", k, ".controls.gen"), h = F, sep = " ") %>% as.data.frame() -> gen
} else if(k != 1){
fread(paste0(path, "chr1_block_", i, "_perm_", j, "_k_", k, ".controls.gen"), h = F, sep = " ") %>% as.data.frame() %>% select(.,-V1:-V5) %>% cbind(gen, .) -> gen
}
}

} else if(test){
k <- 1

gen <- fread(paste0(path, "chr1_block_", i, "_perm_", j, "_k_", k, ".controls.gen"), h = F, sep = " ") %>% as.data.frame()
}

colnames(gen) <- paste0("V",1:ncol(gen))
summary <- fread(summary.file, h = T, sep = " ")
analyze <- function(i = double(),
j = double(),
mode = "default",
path.base = "/scratch/hpc2862/CAMH/perm_container/container_",
summary.file = "/scratch/hpc2862/CAMH/perm_container/snp_summary2.out",
output = "~/repos/coR-ge/data/test_run2.txt",
test = TRUE,
safe = TRUE,
local = FALSE,
h2 = 0.45,
pc = 0.5,
pnc = 0.5,
nc = 1000,
gen = NULL,
summary = summary,
maf = FALSE,
maf_range = NULL){

if(F){ # This is just here to easily assign variables in interactive mode

mode = "default"
path.base = "/scratch/hpc2862/CAMH/perm_container/container_"
summary.file = "/scratch/hpc2862/CAMH/perm_container/snp_summary2.out"
output = "~/repos/coR-ge/data/test_run2.txt"
test = TRUE
safe = TRUE
local = FALSE
h2 = 0.45
pc = 0.5
pnc = 0.5
nc = 1000
gen = NULL
summary = summary
maf = FALSE
maf_range = NULL

}

# ___ __ _ _
# / \ ___ / _| __ _ _ _ | || |_
# / /\ / / _ \| |_ / _` || | | || || __|
# / /_// | __/| _|| (_| || |_| || || |_
# /___,' \___||_| \__,_| \__,_||_| \__|
#


if(is.null(mode) || mode == "default"){
if(mode == "default"){


message("Selecting Causal SNPs")
Expand Down