lynchsynpedsnotebook/LynchvsCephMutationRates.Rmd at main · laurelhiatt/lynchsynpedsnotebook · GitHub

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---
title: "LynchvsCephMutationRates"
author: "Laurel Hiatt"
date: "3/24/2022"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Brief Overview of Data

Both data sets are comprised of autosomal SNVs/autosomal callable fractions,
matched to sample and then with added sample source.

```{r data}
setwd('/Users/quinlan/Documents/Quinlan-PhD/lynchsynpedsnotebook')
list.files()
Lynchdata = read.table("LynchMutsOverCallable.csv", header = TRUE, sep = ',')
Cephdata = read.table("CephMutsOverCallable.csv", header = TRUE, sep = ',')
library(ggplot2)
library(cowplot)

```

## Comparison Plot

```{r Boxplot, echo=FALSE}
lynch <- data.frame(group = "lynch", value = Lynchdata)
ceph <- data.frame(group = "ceph", value = Cephdata)

plotdata <- rbind(lynch,ceph)

ggplot(plotdata) + geom_boxplot(aes(x = group, y = (value.mut_over_callable/2))) + xlab('') + ylab('Mutation Rates') + theme_cowplot()  + geom_jitter(aes(x = group, y = (value.mut_over_callable/2), color = value.source))
```

# Multiplying by Genome for Counts Approximation

```{r Normalizingdata, echo=FALSE}
Lynchdata$approximatecounts = (Lynchdata$mut_over_callable*5750003044)
Cephdata$approximatecounts = (Cephdata$mut_over_callable*5750003044)
# calculated from autosomal chromosome bed file, summed and * 2 for diploid
lynch <- data.frame(group = "lynch", value = Lynchdata)
ceph <- data.frame(group = "ceph", value = Cephdata)

plotdata <- rbind(lynch,ceph)

ggplot(plotdata) + geom_boxplot(aes(x = group, y = (value.approximatecounts/2))) + xlab('') + ylab('Approximate Mutations') + theme_cowplot() + geom_jitter(aes(x = group, y = (value.approximatecounts/2), color = value.source)) + geom_hline(yintercept=70.1, color = 'red', linetype = 'dashed')
#70.1 from sasani paper, average number of mutations for haploid genome

ggplot(plotdata) + geom_boxplot(aes(x = group, y = (value.approximatecounts/2))) + xlab('') + ylab('Mutation Rates') + theme_cowplot() + theme(legend.position="none") + geom_jitter(aes(x = group, y = (value.approximatecounts/2)))

ggplot(plotdata) + geom_boxplot(aes(x = group, y = (value.approximatecounts/2))) + xlab('') + ylab('Approximate Mutations') + theme_cowplot() + geom_jitter(aes(x = group, y = (value.approximatecounts/2), color = value.source)) + geom_hline(yintercept = 70, linetype= 'dotted', color = 'red')

```

```{r statistics}

t.test(Lynchdata$mut_over_callable, Cephdata$mut_over_callable)
```