estill_novakovic_comparison.Rmd

---
title: "Comparison of GMEA+Mitch results of Estill and Novakovic"
author: "The methylation in ART meta-analysis group"
date: "`r Sys.Date()`"
output:
  html_document:
    fig_width: 7
    fig_height: 7
  toc: true
theme: cosmo
---

```{r,packages}

source("meth_functions.R")

```

## Introduction

The purpose of this is to compare the GMEA results of Estill and Novakovic studies.

estill_gmeapr_nat_vs_fh.tsv  novakovic_gmeapr_nat_vs_fh.tsv
estill_gmeawg_nat_vs_fh.tsv  novakovic_gmeawg_nat_vs_fh.tsv

```{r,load}

eswg <- read.table("estill_gmeawg_nat_vs_fh.tsv")
nowg <- read.table("novakovic_gmeawg_nat_vs_fh.tsv")

head(eswg)
head(nowg)

eswg$metric <- sign(eswg$median) * eswg$sig
nowg$metric <- sign(nowg$median) * nowg$sig

x <- merge(eswg,nowg,by=0)
x <- x[,c("Row.names","metric.x","metric.y")]
rownames(x) <- x[,1]
x[,1] = NULL
colnames(x) <- c("estill","novakovic")

mylm <- lm(x[,1] ~ x[,2])
plot(x,xlim=c(-25,10),main="GMEA score")
grid()
abline(mylm,col="red",lty=2)

abline(h=-5,col="blue")
abline(v=-5,col="blue")

# spearman
cor(x[,1],x[,2],method="s")

# pearson
cor(x[,1],x[,2],method="p")

```


```{r,sorting}

subset(x, estill < -5 & novakovic < -5)

x2 <- subset(x, estill < -5 & novakovic < -5)

x2 <- x2[order(rowMeans(x2)),]

x2 %>%  kbl(caption = "Top genes detected with GMEA") %>% kable_paper("hover", full_width = F)

```


```{r,mitch}

head(x2)

library("mitch")
genesets <- gmt_import("ReactomePathways.gmt")

res <- mitch_calc(x, genesets, priority="effect")

head(res$enrichment_result,20) %>%
    kbl(caption = "Top genes detected with GMEA") %>%
    kable_paper("hover", full_width = F)

mitch_report(res,outfile="gmea_mitch.pdf")

```


```{r,session}

sessionInfo()

```