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This repository contains data and scripts used in the paper

Dissecting vancomycin intermediate resistance in Staphylococcus aureus using genome-wide association Md Tauqeer Alam; Robert A. Petit III; Emily K. Crispelll III; Timothy A. Thornton; Karen N. Conneely; Yunxuan Jiang; Sarah W. Satola; Timothy D. Read Genome Biology and Evolution 2014; doi: 10.1093/gbe/evu092

WEBSITE

We have published an interactive webserver to help exploration of the data. The site was built using the RStudio Shiny package.

SCRIPTS

visa-table-manipulation.R
Script to automate rare mutation counting.
visa_gwas.R
Script to automate ROADTRIPS and QROADTRIPS analysis using E-Test values.
visa_gwas_bmd.R
Script to automate ROADTRIPS and QROADTRIPS analysis using BMD values.
visa_gwas_pap-auc.R
Script to automate ROADTRIPS and QROADTRIPS analysis using PAP-AUC values.
visa_gwas_functions.R
Script containing functions for process data to be used with ROADTRIPS and 
QROADTRIPS.
Interactive_VISA_model
This directory contains scripts, data and tests for the shiny interactive website.

DATA

superAlignProt124.phy
Alignment of core genes
superAlignDNA124.phy
Alignment of core proteins
superAlignDNA124.fna
Alignment of core proteins
VISA_feature_table.xls
Created by subsetting the SNP matrix by the 16 candidate genes.  Also added 
in the vector of SNP frequency for in the Staph genome database.
VISA-feature-table-v2-PAPAUC
Transpose VISA_feature_table.xls and manually removed all SNPs with a count 
> 81 (ie common SNPs).  Add PAP-AUC data. Used to make prelim version of 
candidate SNP frequency table.
VISA-feature-table-v2-etest
From VISA-feature-table-v2-PAPAUC but used for Etest counts.
VISA-feature-table-v3.csv
Adapted from VISA-feature-table-v2-etest.  Stripped out unnecessary fields.  This is the input file for the Shiny server and the random forest model. (Note - this was moved into the interactive_VISA_model directory in order to publish the webserver.)
genotype.txt
A matrix of SNPs for the total 75 samples.
phenotype.txt
Phenotype values from E-Test for each sample.
phenotype_bmd.txt
Phenotype values from BMD for each sample.
phenotype_pap-auc.txt
Phenotype values from PAP-AUC for each sample.