pairs.Rmd

---
title: "pair code"
output: html_document
---

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


```{r, eval=F}
source('./shreyas_analysis_files/sero_mc_st.R')
source('./shreyas_analysis_files/sero_mc_cc.R')
```

```{r, eval=F}
source('./shreyas_analysis_files/sero_cc_mb.R')
source('./shreyas_analysis_files/sero_cc_mb.R')

```

Index to identify serotype pairs found more often than expected
```{r}
source('./shreyas_analysis_files/ss_results.R')

index.more <- read.csv('./shreyas_analysis_files/ss_index.csv')
index.more <- index.more[order(-index.more$total),]
View(index.more[,c('sero_pair','total')])

write.csv(index.more, 'st.pairs.over.csv')
```

Index to identify serotype pairs found LESS often than expected
```{r}
source('./shreyas_analysis_files/ss_results_LESS.R')

index.less <- read.csv('shreyas_analysis_files/ss_index_under_rep.csv')

index.less <- index.less[order(-index.less$total),]
View(index.less[,c('sero_pair','total')])

write.csv(index.less, 'st.pairs.under.csv')

```


Network plot

```{r}
source('./shreyas_analysis_files/index_network_plot.R')

```