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DEG_analysis.Rmd
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DEG_analysis.Rmd
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---
title: "DEG_analysis"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{DEG_analysis}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
```{r setup}
library(RNAseqStat)
```
## DEG analysis
DEG analysis will be run by limma edgeR and DESeq2 in this step.
```{r eval=FALSE}
deg_run(counts_input,group_list,test_group = "T", control_group = "C",dir = results_dir)
```
# Resluts Overview
```{r include=FALSE}
fl <- list.files("../dev/example_output/")
modules <- fl[grep("2-DEG_DEseq2",fl)]
bitmap_l <- lapply(modules, function(x){
pdftools::pdf_render_page(glue::glue("../dev/example_output/{x}"), page = 1, dpi = 300)
})
basenames <- gsub(pattern = "\\.pdf$", "", modules)
names(bitmap_l) <- basenames
tmp <- lapply(seq_along(bitmap_l), function(x){
png::writePNG(bitmap_l[[x]], glue::glue("{names(bitmap_l)[[x]]}.png"))
})
```
```{r qc, echo=FALSE, out.width="100%", fig.show='hold', fig.cap='QC'}
knitr::include_graphics("2-DEG_DEseq2_qc_dispersions.png")
```
```{r rawvsnorm, echo=FALSE, out.width="100%", fig.show='hold', fig.cap='RAWvsNORM'}
knitr::include_graphics("2-DEG_DEseq2_RAWvsNORM.png")
```
```{r top100, echo=FALSE, out.width="100%", fig.show='hold', fig.cap='Top100'}
knitr::include_graphics("2-DEG_DEseq2_top100_heatmap.png")
```
```{r volcano, echo=FALSE, out.width="100%", fig.show='hold', fig.cap='Volcano'}
knitr::include_graphics("2-DEG_DEseq2_volcano.png")
```