SNPhood (version 1.2.3)

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

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

"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))