README.Rmd

---
title: "cellatacUtils"
output: github_document
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  cache = FALSE,
  message = FALSE,
  warning = FALSE
)
```

R package for handling [cellatac pipeline](https://github.com/cellgeni/cellatac) output 

## Installation
```{r, eval=FALSE, echo=TRUE}
devtools::install_github("emdann/cellatacUtils")
```


## Example usage

Load pipeline output as Seurat object

```{r, eval=FALSE, echo=TRUE}
library(cellatacUtils)
results.dir <- "path/to/results"
cellatac.seu <- load_cellatac_seurat(results.dir)
```

Calculate QC metrics for peaks

```{r, eval=FALSE, echo=TRUE}
## Load Ensembl based annotation from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("EnsDb.Hsapiens.v86")
library(EnsDb.Hsapiens.v86)

## Load Signac for ENCODE blacklist annotation
library(Signac)

cellatac.seu <- compute_peakQC(cellatac.seu, 
                               cluster_col = "seurat_clusters", 
                               EnsDb.genome = EnsDb.Hsapiens.v86, 
                               blacklist_gr = blacklist_hg38)
```

Calculated peak QC metrics:

* tot_count: total count of fragments overlapping peak
* tot_cells: total number of cells in which peak is accessible
* frac_cells: fraction of cells in which peak is accessible
* max_frac: maximum percent of cells with accessible peak in any given cluster (to filter out peaks that are not observed to be accessible in at least n% cells of cells in at least one cluster)
* peak_width: width of peak in bps
* exon: is peak overlapping exon?
* intron: is peak overlapping intron?
* promoter: is peak overlapping promoter?
* annotation: annotation of overlapping genomic region (promoter, exon, intron, intergenic)
* gene_name: name of overlapping gene (downstream gene for promoter region, NA for intergenic peaks)
* gene_id: ENSEMBL id of overlapping gene (downstream gene for promoter region, NA for intergenic peaks)
* tss_distance: distance to closest Transcription Start Site in bps
* ENCODE_blacklist: is peak overlapping ENCODE blacklist region?