aging-biomarkers.Rmd

---
title: "Aging Biomarkers"
author: "Petr Simecek"
output: html_document
---

```{r read-chunk, include=FALSE, cache=FALSE}
knitr::read_chunk("chunks.R")
```

```{r knitr-opts-chunk, include=FALSE}
```

**Last updated:** `r Sys.Date()`

**Code version:** `r workflowr::extract_commit(".", 1)$sha1`

## Cdkn2a

```{r}
kidney = new.env()
heart = new.env()
load("../../kidney2/R/DO188b_kidney_noprobs.RData", env=kidney)
load("../../heart2/DO189_heart_v2_noprobs.RData", env=heart)

suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(ggsci))
theme_set(theme_bw())

pval.output <- function(p) {
  if (p<0.001) 
    return("< 0.001") 
  else 
    paste("=",round(p,3))
}

# for some reasons, heart SN are characters
heart$annot.samples$Sample.Number <- as.numeric(heart$annot.samples$Sample.Number)

sn <- intersect(kidney$pca1$Sample.Number, heart$pca1$Sample.Number)
kidney$idx <- match(sn, kidney$pca1$Sample.Number)
heart$idx <- match(sn, heart$pca1$Sample.Number)

sel.gene <- "Cdkn2a"
sel.kidney <- which(kidney$annot.mrna$symbol == "Cdkn2a")
sel.heart <- which(heart$annot.mrna$symbol == "Cdkn2a")

sel.mrna <- cbind(kidney$annot.samples[kidney$idx, ], 
              Kidney = kidney$expr.mrna[kidney$idx, sel.kidney],
              Heart = heart$expr.mrna[heart$idx, sel.heart])
sel.mrna$Age <- factor(mrna$Age, levels = c(6,12,18))

ggplot(sel.mrna, aes(x = Kidney, y = Heart, color = Age, shape=Sex, group=Age)) +
  geom_point() +
  geom_smooth(method="lm", se=FALSE, size=0.2) +
  labs(title = "Protein Expression") +
  scale_color_uchicago() + labs(title="Cdkn2a")

```


## Session information

<!-- Insert the session information into the document -->
```{r session-info}
```