SignatureSet: Class to Contain Signature Definitions

In Nanostring-Biostats/NanoStringNCTools: NanoString nCounter Tools

Class to Contain Signature Definitions

Description

The SignatureSet class defines gene-based signatures.

Usage

  SignatureSet(weights = NumericList(), groups = factor(), func = character(), 
               version = character(), ...)

Arguments

weights	A named NumericList defining signatures based on linear combinations of genes.
groups	A factor vector indicating groups in the SignatureSet
func	Character indicating function to use
version	Character indicating version to use
...	Additional arguments for future use.

Value

A SignatureSet object

Utilities

length(x)

returns the number of signatures in x.

lengths(x, use.names = TRUE)

returns a named integer vector containing the number of genes in each of the signatures in x.

names(x)

returns a character vector containing the signature names in x.

weights(object)

returns a named NumericList that defines the linear combination based signatures.

weights(object) <- value

replaces the NumericList that defines the linear combination based signatures.

getSigFuncs(object)

returns the signature functions of an object.

groups(object)

returns a factor vector representing the signature groups.

groups(object) <- value

replaces the factor vector representing the signature groups.

version(object)

: returns the signature version.

Author(s)

Patrick Aboyoun

See Also

NanoStringRccSet

Examples

SignatureSet(weights=list(x = c(a = 1),
                          y = c(b = 1/3, d = 2/3),
                          z = c(a = 2, c = 4)),
             groups=factor("x", "y", "z"),
             func = c(x="default", y="default", z="default"))

Nanostring-Biostats/NanoStringNCTools documentation built on Dec. 18, 2024, 1:24 a.m.