counts-method: Extract count data from a 'SNPhood' object.

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

Description

counts extracts count 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. Either the count data for the unbinned or binned SNP regions can be extracted.

Usage

## S4 method for signature 'SNPhood'
counts(object, type = "binned", readGroup = NULL,
  dataset = NULL, ...)

Arguments

object	Object of class SNPhood
type	Character(1). Default "binned". Either "binned" or "unbinned" to extract counts after or before binning the SNP regions, respectively.
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).
...	not used

Value

A named nested list with the requested count data, organized after read group and dataset.

See Also

SNPhood, enrichment

Examples

data(SNPhood.o, package="SNPhood")
str(counts(SNPhood.o))
str(counts(SNPhood.o, readGroup = "paternal", dataset = 1))
str(counts(SNPhood.o, readGroup = c("maternal", "paternal"), dataset = 1))

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