enrichmentAtAnnotation: Enrichment of (combinatorial) states for genomic annotations

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

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

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.