STARRseqData-class: Class '"STARRseqData"'

In BasicSTARRseq: Basic peak calling on STARR-seq data

Description

The STARR-seq data class is a container for STARR-sequencing data.

Details

STARRseqData contains two GRanges objects that store the STARR-seq sequences and the input sequences respectively of an STARR-seq experiment.

Slots

sample:

Object of class "GRanges" which contains STARR-seq sequences.

control:

Object of class "GRanges" which contains input sequences.

Constructor

STARRseqData(sample, control): Create a STARRseqData object.

sample:

An GRanges object.

control:

An GRanges object.

Accessors

In the following code snippets, x is an STARRseqData object.

sample(x), sample(x) <- value:

Get or set the STARR-seq sequences.

control(x), control(x) <- value:

Get or set the input sequences.

Methods

getPeaks

signature(object = "STARRseqData"): Performs basic peak calling on data.

Author(s)

A. Buerger

References

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq. Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science.1232542. Epub 2013 Jan 17.

See Also

GRanges getPeaks

Examples

# create small sample dataset
starrseqFileName <- system.file("extdata", "smallSTARR.bam", package="BasicSTARRseq")
inputFileName <- system.file("extdata", "smallInput.bam", package="BasicSTARRseq")
STARRseqData(sample=starrseqFileName, control=inputFileName, pairedEnd=TRUE)

BasicSTARRseq documentation built on Nov. 8, 2020, 5:58 p.m.