STARRseqData-class {BasicSTARRseq} | R Documentation |
"STARRseqData"
The STARR-seq data class is a container for STARR-sequencing data.
STARRseqData contains two GRanges objects that store the STARR-seq sequences and the input sequences respectively of an STARR-seq experiment.
sample
:Object of class "GRanges"
which contains STARR-seq sequences.
control
:Object of class "GRanges"
which contains input sequences.
STARRseqData(sample, control)
: Create a STARRseqData object.
sample
:An GRanges object.
control
:An GRanges object.
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.
signature(object = "STARRseqData")
: Performs basic peak calling on data.
A. Buerger
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.
# 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)