TF.Rmd

---
title: "Transcription factors"
output: 
  html_document:
    code_folding: hide
---


```{r library, echo=TRUE,warning=FALSE,message=FALSE,error=FALSE, include=FALSE}
library(pheatmap)
library(tidyverse)
source('functions.R')
library(yaml)
```


```{r yaml, echo=TRUE,warning=FALSE,message=FALSE,error=FALSE, include=FALSE}
params <- read_yaml("config.yml")
```

# Transcription factor analysis

The aim of this code is to subset each transcription factor from your significant results and place the results of that into the folder TranscriptionFactors/

```{r tr, echo=TRUE,warning=FALSE,message=FALSE,error=FALSE, include=FALSE}
TF <- read.csv("TF.csv", header = T)
TF <- TF %>% dplyr::filter(X == "Yes") %>% dplyr::select(Name)


design_files <- list.files(path="results", pattern = "(design_)*res\\.csv$")

for (i in design_files) {
 df <- read.csv(paste0("results/",i), header=T)
 df_new <- subset(df, toupper(SYMBOL) %in% toupper(TF$Name))
 dir.create(file.path("TranscriptionFactors"), showWarnings = FALSE)
 write.csv(df_new, file=paste0("TranscriptionFactors/",i))
  }
```