enrichmentAtAnnotation {chromstaR} | R Documentation

## Enrichment of (combinatorial) states for genomic annotations

### Description

The function calculates the enrichment of a genomic feature with peaks or combinatorial states. Input is a `multiHMM` object (containing the peak calls and combinatorial states) and a `GRanges-class` object containing the annotation of interest (e.g. transcription start sites or genes).

### Usage

    enrichmentAtAnnotation(
      bins,
      info,
      annotation,
      bp.around.annotation = 10000,
      region = c("start", "inside", "end"),
      what = "combinations",
      num.intervals = 21,
      statistic = "fold"
    )

### Arguments

`bins` | The `$bins` entry from a `multiHMM` or `combinedMultiHMM` object.
`info` | The `$info` entry from a `multiHMM` or `combinedMultiHMM` object.
`annotation` | A `GRanges-class` object with the annotation of interest.
`bp.around.annotation` | An integer specifying the number of basepairs up- and downstream of the annotation for which the enrichment will be calculated.
`region` | A combination of `c('start','inside','end')` specifying the region of the annotation for which the enrichment will be calculated. Select `'start'` if you have a point-sized annotation like transcription start sites. Select `c('start','inside','end')` if you have long annotations like genes.
`what` | One of `c('combinations','peaks','counts')` specifying on which feature the statistic is calculated.
`num.intervals` | Number of intervals for enrichment 'inside' of annotation.
`statistic` | The statistic to calculate. Either 'fold' for fold enrichments or 'fraction' for fraction of bins falling into the annotation.

### Value

A `list()` containing `data.frame()`s for enrichment of combinatorial states and binary states at the start, end and inside of the annotation.

### Author(s)

Aaron Taudt

[Package chromstaR version 1.20.2 Index]