24 lines
931 B
R
24 lines
931 B
R
# Lab 6 for the University of Tulsa's CS-6643 Bioinformatics Course
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# GWAS
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# Professor: Dr. McKinney, Fall 2022
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# Noah L. Schrick - 1492657
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## Set Working Directory to file directory - RStudio approach
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setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
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#### Part 0: PLINK
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if (!require("BiocManager")) install.packages("BiocManager")
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library(BiocManager)
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if (!require("snpStats")) BiocManager::install("snpStats")
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library(snpStats)
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ex.data <- read.pedfile(file="extra.ped", snps="extra.map")
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ex.data$fam
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phenotype <- ex.data$fam$affected-1 # change pheno from 1/2 to 0/1
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genotypes <- ex.data$genotypes # encoded as AA/AB/BB
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snp.ids <- as.character(ex.data$map$snp.names)
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genotypes.df <- data.frame(as(genotypes, "character"))
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colnames(genotypes.df) <- snp.ids
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# observed contingency table for SNP rs630969
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table(phenotype,genotypes.df$rs630969,
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dnn=c("phenotype","genotype")) # dnn dimension names of table |