regi-methods {ChIPQC} | R Documentation

## Retrieve genomic profile information

### Description

Retrieve genomic profile information in terms of relative enrichment over background genomic distribution.

### Methods

`signature(object = "ChIPQCexperiment")`

  Retrieve a `matrix` of relative enrichment values for a variety of genomic features. Each column represents the enrichment values for one sample in the experiment.

`signature(object = "list")`

  Retrieve a `matrix` of relative enrichment values for a variety of genomic features. Each column represents the enrichment values for one sample in a list of ChIPQCsample objects.

`signature(object = "ChIPQCsample")`

  Retrieve a `vector` of relative enrichment values for a variety of genomic features for a sample. Relative enrichment is computed as the proportion of reads overlapping a genomic feature type compared to the overall proportion of base pairs in the genome comprising those features. Genomic features include:

  3UTRs | 3' UTRs
  5UTRs | 5' UTRs
  Introns | Intronic (non-coding) portions of gene bodies
  Transcripts | Transcribed regions, including exons
  Promoters500 | 500bp regions immediately upstream of annotated TSSs
  Promoters2000to500 | 2500bp regions from 2000bp immediately upstream of annotated TSSs to 500bp downstream
  Promoters20000to2000 | 22000bp regions from 20000bp immediately upstream of annotated TSSs to 2000bp downstream

### Author(s)

Thomas Carroll and Rory Stark

### See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

### Examples

    data(example_QCexperiment)
    genomicprofile = regi(exampleExp)
    heatmap(genomicprofile)
    regi(QCsample(exampleExp,1))

[Package ChIPQC version 1.23.1 Index]