SHARP-match-gex-exposome-proteome.Rmd

---
title: "SHARP-match-gex-exposome-proteome"
author: "ks"
date: "6/25/2021"
output: html_document
---

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

## R Libraries

```{r rlibraries}
library(tidyverse)
```

## Load data
```{r  data}
load("data/mgex.RData")
dim(mgex)
load("data/proteome.Rdata")
dim(proteome)
load("data/exposome.RData")
```

Find subset of individuals with expression, proteome and exposome.

```{r common-ids}
isctids <- intersect(covariates$ID,sampleNames(mgex))
length(isctids)
isctids <- intersect(isctids, sampleNames(proteome))
length(isctids)

expsm  <- exposome %>%
          filter(is.element(ID,isctids))
covars <- covariates %>%
          filter(is.element(ID,isctids))
phenos <- phenotype  %>%
          filter(is.element(ID,isctids))
```

## ----order-mgex-measures----------------
```{r database}
#identical(covars$ID,sampleNames(mgex))
helix <- list()
helix$covars <- covars
# add phenotype data
helix$phenos <- phenos
identical(as.character(helix$covars$ID),
          as.character(helix$phenos$ID))
# add expression data
helix$E <- exprs(mgex)
helix$E <- helix$E[,as.character(helix$covars$ID)]
identical(as.character(helix$covars$ID),
          colnames(helix$E))
# add expression pData
helix$pDataE <- pData(mgex)
helix$pDataE <- 
    helix$pDataE[as.character(helix$covars$ID),]
identical(as.character(helix$covars$ID),
          as.character(helix$pDataE$ID))

# add exposome data
identical(as.character(expsm$ID),
          colnames(helix$E))
rownames(expsm) <- expsm$ID
helix$expsm <- expsm[,-1]
identical(rownames(helix$expsm),
          as.character(helix$pDataE$ID))
# add proteome data
helix$prtm <- exprs(proteome)
helix$prtm <- 
    helix$prtm[,as.character(helix$covars$ID)]
identical(as.character(helix$covars$ID),
          colnames(helix$prtm))

save(helix,file="helix.RData")
save(codebook,file="codebook.RData")

# add dnam??
```