rgsets {hypeR}R Documentation

A relational genesets object

Description

A relational genesets object

A relational genesets object

Arguments

genesets

A list of genesets where list names refers to geneset labels and values are geneset members represented as a vector

nodes

A data frame of labeled nodes e.g.

label
G1 Geneset 1
G2 Geneset 2
G3 Geneset 3
edges

A data frame of directed edges

from to
G1 G2
G1 G3
name

A character vector describing source of genesets

version

A character vector describing versioning

Methods

print(rgsets) shows some information about the object data

rgsets$subset(labels) returns an rgsets object subsetted on geneset labels

See Also

gsets pvector

Methods

Public methods


Method new()

Usage
rgsets$new(genesets, nodes, edges, name = "", version = "", quiet = FALSE)

Method print()

Usage
rgsets$print(...)

Method reduce()

Usage
rgsets$reduce(background)

Method subset()

Usage
rgsets$subset(labels)

Method clone()

The objects of this class are cloneable with this method.

Usage
rgsets$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

testdat <- readRDS(file.path(system.file("extdata", package="hypeR"), "testdat.rds"))
rgsets <- rgsets$new(genesets=testdat$genesets, nodes=testdat$nodes, edges=testdat$edges, name="Example", version="v1.0")


[Package hypeR version 1.4.0 Index]