R Notebook

library(tidyr)
library(ggplot2)
setwd("/Users/peter/Documents/BIO340R")
results<-read.table("Combined_8_D21_out.qassoc", header = TRUE, stringsAsFactors = FALSE) 

Import association data containing both Drosophila genders’ polymorphism/survival data at day 21 of experiment.

results<-separate(results,SNP,c("chrom","pos","type"),sep = "_")
results$pos<-as.numeric(results$pos)
results$log<- -log10(results$P)
POS<-results$pos
logp<-results$log
chm<-factor(results$chrom)

Seaprate data by underscore into chromosome, position, and type. Plot p-values of each polymorphism at -log10(p).

g<-ggplot(results) +
  geom_point(aes(POS, logp, colour=chm))+
  labs(y="-log10 (p-value)",x="Base Pair Position", title = "Manhattan Plot")+
  theme(axis.text.x=element_blank())

g+facet_grid(cols=vars(results$chrom))+geom_hline(aes(yintercept=5))

g+facet_grid(rows = vars(results$chrom))+geom_hline(aes(yintercept=5))

Create Manhattan plot of polymorphisms separated by Chromosome. 11 significant polymorphisms found. 8 are intragenic, 3 are intergenic. 1 is non-coding. The 8 intragenic were found to be in 7 different genes.