# Lab 6 for the University of Tulsa's CS-6643 Bioinformatics Course
# GWAS
# Professor: Dr. McKinney, Fall 2022
# Noah L. Schrick - 1492657

## Set Working Directory to file directory - RStudio approach
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))

#### Part 0: PLINK
if (!require("BiocManager")) install.packages("BiocManager")
library(BiocManager)
if (!require("snpStats")) BiocManager::install("snpStats")
library(snpStats)

ex.data <- read.pedfile(file="extra.ped", snps="extra.map")
ex.data$fam
phenotype <- ex.data$fam$affected-1  # change pheno from 1/2 to 0/1
genotypes <- ex.data$genotypes       # encoded as AA/AB/BB
snp.ids <- as.character(ex.data$map$snp.names)
genotypes.df <- data.frame(as(genotypes, "character"))
colnames(genotypes.df) <- snp.ids
# observed contingency table for SNP rs630969
table(phenotype,genotypes.df$rs630969,
      dnn=c("phenotype","genotype")) # dnn dimension names of table 
dim(genotypes.df)

#### Part A: Chi-Square Test
# creates list of observed contingency tables for all SNPs
# sapply acts on each column of genotypes.df
observed.tables.list <- sapply(genotypes.df, function(x) 
  table(phenotype,x,dnn=c("phenotype","genotype")))

test.table <- observed.tables.list$rs634228
genoMarg.vec  <-  colSums(test.table)           # margin vector
phenoMarg.vec <- rowSums(test.table)            # margin vector        
totalSubj <- sum(genoMarg.vec)                  # total subjects
expect.test <- outer(phenoMarg.vec,genoMarg.vec/totalSubj,'*')

## Fisher Test
# Fisher exact test (chi-square test) for all SNPs
fish_fn <- function(i){  
  cbind(snp.ids[i], fisher.test(observed.tables.list[[i]])$p.value)    
}

# apply fisher exact test to all SNPs
fish.df <- data.frame(t(sapply(1:ncol(genotypes.df), fish_fn)))
colnames(fish.df) <- c("rs", "p_value")

# sort SNPs by Fisher exact p-value
if (!require("dplyr")) install.packages("dplyr")
library(dplyr)
fish.results <- fish.df                            %>% 
  mutate_at("p_value", as.character) %>%
  mutate_at("p_value", as.numeric)   %>%
  arrange(p_value) 
print(fish.results)