Finalizing Part 0

.~lock.lab_gwas_stats.docx#

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+,noah,NovaArchSys,20.10.2022 16:12,file:///home/noah/.config/libreoffice/4;

Schrick-Noah_CS-6643_Lab-6.R

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+# 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