ChIPQC (version 1.8.2)

regi-methods: 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 = "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

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

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