SignatureFeatures-methods: Signature Features

In hdsu-bioquant/ButchR: Non-Negative Matrix Factorization Suite

Signature Features

Description

Returns a binary matrix for every factorization rank, with features in the rows and samples in the columns, in which 1 means that the features is contributing to the signature, and 0 it does not. The extraction of Signature Features is not supported for k = 2.

Usage

SignatureFeatures(x, k = NULL, ...)

## S4 method for signature 'ButchR_NMF'
SignatureFeatures(x, k = NULL, ...)

## S4 method for signature 'ButchR_integrativeNMF'
SignatureFeatures(x, k = NULL, view_id = NULL, ...)

Arguments

x	an object of class ButchR_NMF, ButchR_joinNMF, or ButchR_integrativeNMF.
k	numeric - factorization rank
...	additional parameters.
view_id	character vector with views from which signature features will be extracted.

Value

list of binary matrices if 'k'=NULL or a single binary matrix for the selected factorization rank.

Examples

data("leukemia")
nmf_exp <- run_NMF_tensor(leukemia$matrix, ranks = 3,
                             method = "NMF",
                             n_initializations = 2,
                             extract_features = TRUE)
SignatureFeatures(nmf_exp)
SignatureFeatures(nmf_exp, k = 3)
## Not run: 
# For ButchR_NMF objects:
SignatureFeatures(nmf_exp)
SignatureFeatures(nmf_exp, k = 3)

## End(Not run)
## Not run: 
# For ButchR_integrativeNMF objects:
SignatureFeatures(inmf_exp, k = 3)

## End(Not run)

hdsu-bioquant/ButchR documentation built on Jan. 28, 2023, 6:06 p.m.