enrichment-methods: Extract enrichment data from an object.

In SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

Description

Extract enrichment data from an object.

enrichment extracts enrichment data from a SNPhood object. The full count data or only a subset can be extracted by settings the parameters type, readGroup and dataset accordingly. Principally, either the count data for the unbinned or binned SNP regions can be extracted.

Usage

enrichment(object, ...)

## S4 method for signature 'SNPhood'
enrichment(object, readGroup = NULL, dataset = NULL,
  ...)

Arguments

object	An object containing enrichment information.
...	Additional arguments, for use in specific methods.
readGroup	Character(1). Default NULL. Read group that should be plotted, specified by its name as obtained by the function annotationReadGroups). If only one read group is defined in the object, this may also be NULL for user conveniance.
dataset	Numeric(1) or Character(1). Single dataset that should be used for plotting, either specified as integer (such as 1, value must be between 1 and the total number of datasets as defined in the object) or its annotation (name must appear in the dataset names as obtained via the function annotationDatasets).

Value

Enrichment of the object or the objects components.

Named list with the requested enrichment matrices from the SNPhood object, organized by read group and dataset

See Also

counts

Examples

data(SNPhood.o, package="SNPhood")
str(enrichment(SNPhood.o), list.len=5)

SNPhood documentation built on Nov. 8, 2020, 6:22 p.m.