view deseq2_02_results.Rmd @ 2:706ecfe0bac3 draft

initial 2.2.0

---
title: 'DESeq2 Analysis'
output: html_document
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = as.logical(opt$X_e), 
  error = TRUE
)
```


## Results

```{r}
res = results(dds, contrast = c(opt$X_D, opt$X_E, opt$X_F), alpha = opt$X_I)
DT::datatable(as.data.frame(res))
```

```{r}
# significant genes
sig_res = res[(res$padj < opt$X_I) & !is.na(res$padj), ]
write.csv(sig_res, file = paste0(opt$X_d, '/significant_genes.csv'), quote = FALSE)
```

```{bash echo=FALSE}
cp ${X_d}/significant_genes.csv ${X_J}
```