In epwilliams23/Final-Project: SNP Mapper

Introduction

SNPs found throughout the genome of viruses are of great importance to virologist as it can tell one about the mutations a virus is undergoing as it transends different host barriers or to observe which parts of the genome are conserved. With this said, this R package will allow one to visually represent SNPs found in the virus genomes.

SNP.mapper contains 2 functions, the first function will create a plot where SNP frequency (Percentage) will be plotted against the length of the genome (Nucleotide Position), the second function will create a plot where the number of observed SNPs (Number of SNPs) at each passage will be plotted against passage number(Passage Number).

Funtions

frpo_plot function

Creates a plot where SNP frequency (Percentage) will be plotted against the length of the genome (Nucleotide Position).

map_SNP function

Creates a plot where the number of observed SNPs (Number of SNPs) at each passage will be plotted against passage number(Passage Number).

Data needed for Functions

frpo_plot function

Funtion requires a data frame where the first column contains the frequency of a SNP (frequency) corresponding to second column containing the position of the SNP on the genome (position).

|position|frequency| |--------|---------| |x|y|

map_SNP function

Function requires a data frame where first column contains the Number of SNPs (snps) corresponding to the 2nd column containing the segment (segment) corresponding to the 3rd column containg the passage number (passage).

|passage|snps|segments| |-------|----|--------| |x|y|z|

It is highly recommended that the data originates from viruses which exhibit genomes that consist out of more that 1 segment.

Create the Plot

frpo_plot function

To run the function you may use the example code below:

The user need to specify the length of the genome, the default is 4000 bp.

library(tidyverse)
library(SNP.mapper)

frpo_plot_plot(example.data, 3500)

map_SNP function

To run the function you may use the example code below:

library(tidyverse)
library(SNP.mapper)

map_SNP(example.data2)

epwilliams23/Final-Project documentation built on May 6, 2019, 6:03 p.m.