create_sample_sheet_diffbind.Rmd

---
title: "create sample sheet for diffBind"
author: "Javier Rodriguez Hernaez"
output: flexdashboard::flex_dashboard
---

```{r setup, include=FALSE}
input_dir="/Users/javrodher/Work/RStudio-PRJs/PTCL-project_2023/data/hichip-chip_peaks/"
peakome_file="/Users/javrodher/Work/RStudio-PRJs/PTCL-project_2023/data/peakome_tiled.bed"
ss_file="samples.diffBind.csv"
bam_suffix = "chip_sorted.bam"
peak_suffix = "chip_peaks.broadPeak"
n_cores=8

options(scipen = 999)
knitr::opts_chunk$set(message=FALSE, warning=FALSE, echo=FALSE, results = FALSE)
knitr::opts_knit$set(root.dir = output_dir)
```

```{r}
bams_files = list.files(input_dir,pattern = paste0(bam_suffix,"$"),full.names = F,include.dirs = F,recursive = T)
peak_files = list.files(input_dir,pattern = paste0(peak_suffix,"$"),full.names = F,include.dirs = F,recursive = T)

sampleName_bams=gsub(bams_files,pattern="/chip_sorted.bam",replacement = "")
sampleName_peaks=gsub(peak_files,pattern="/chip_peaks.broadPeak",replacement = "")
sampleName = sampleName_bams[sampleName_bams %in% sampleName_peaks]

if(peakome_file!=F){ peak_files = peakome_file } else { peak_files = paste0(input_dir,"/",peak_files) }
bam_files = paste0(input_dir,"/",bams_files)

ss=data.frame(SampleID=sampleName,
              Tissue=NA,
              Factor=NA,
              Condition=NA,
              Treatment=NA,
              Replicate=NA,
              bamReads=bam_files,
              Peaks=peak_files,
              PeakCaller = "bed",stringsAsFactors = F)
print(ss)
write.csv(ss,paste0(input_dir,"/samples.diffBind.csv"),row.names = F)
```