ml2ESE: Creates an EnrichmentSE from a list of normalizedMatrix...

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

Creates an EnrichmentSE from a list of normalizedMatrix objects

Description

Creates an EnrichmentSE from a list of normalizedMatrix objects

Usage

ml2ESE(ml, rowRanges, assayName = "input", addScore = FALSE, ...)

Arguments

ml	A named list of normalizedMatrix objects with corresponding rows.
rowRanges	An optional GRanges object corresponding to the rows of each object of 'ml'.
assayName	The name of the assay, defaults to 'input'
addScore	Logical; whether to add an enriched_score assay.
...	Passed to 'SummarizedExperiment()'

Examples

# for an example we first need a list of signal matrices. To this end, 
# we first fetch the path to the example bigwig file:
bw <- system.file("extdata/example_atac.bw", package="epiwraps")
# we load example regions:
regions <- rtracklayer::import(system.file("extdata/example_peaks.bed", 
                                           package="epiwraps"))
# we obtain the matrix of the signal around the regions, indicating that we
# want the output as a list of signal matrices:
m <- signal2Matrix(bw, regions, ret="list")
# we can then transform this into an EnrichmentSE object:
m <- ml2ESE(m)

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.