regi-methods: Retrieve genomic profile information

In shengqh/ChIPQC: Quality metrics for ChIPseq data

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))

shengqh/ChIPQC documentation built on Feb. 27, 2023, 10:51 p.m.