TSSenrichment: TSSenrichment

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

TSSenrichment

Description

A common quality metric for ATAC-seq data (see [definition](https://www.encodeproject.org/data-standards/terms/#enrichment) ). The interpretation of the enrichment score depends on the annotation (the score tends to increase when only fewer, more common TSS are used), but according to ENCODE guidelines anything below 5 is of concerning quality, while a score >8 is ideal.

Usage

TSSenrichment(tracks, ensdb, useSeqLevels = NULL)

Arguments

tracks	A (named) vector of paths to bigwig files.
ensdb	An 'ensembldb' object. Alternatively, a GRanges object of regions centered around TSS.
useSeqLevels	Optional seqlevels to use. If NULL, all are used.

Value

A list with the slots 'score' (numeric vector of TSS enrichment scores per sample) and 'data' (per bin enrichment, for plotting)

Examples

# we first fetch the path to the example bigwig file:
bw <- system.file("extdata/example_atac.bw", package="epiwraps")
## normally, we would load an ensembldb object using AnnotationHub. For the 
## purpose of this example, we'll pretend that the following set of regions
## represent TSS:
tss <- system.file("extdata/example_peaks.bed", package="epiwraps")
tss <- rtracklayer::import(tss)
en <- TSSenrichment(bw, tss)
en$score
## you can also plot using something like this:
## ggplot(en$data, aes(position, enrichment, colour=sample)) + geom_line()

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.