SignatureSpecificFeatures-methods: Signature Specific Features

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

Signature Specific Features

Description

Returns the list of signatures specific features for all factorization ranks or for the indicated rank, if return_all_features = TRUE 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 Specific Features is not supported for k = 2

Usage

SignatureSpecificFeatures(x, k = NULL, return_all_features = FALSE, ...)

## S4 method for signature 'ButchR_NMF'
SignatureSpecificFeatures(x, k = NULL, return_all_features = FALSE, ...)

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

## S4 method for signature 'ButchR_joinNMF'
SignatureSpecificFeatures(
  x,
  k = NULL,
  return_all_features = FALSE,
  view_id = NULL,
  ...
)

Arguments

x	an object of class ButchR_NMF, ButchR_joinNMF, or ButchR_integrativeNMF.
k	numeric - factorization rank
return_all_features	logical indicating whether to return a binary matrix with the same dimension as the selected factorization rank. Were a 1 is assigned to those features contributing towards a signature and a 0 to those that do not show a significant contribution.
...	additional parameters.
view_id	character vector with views from which signature specific features will be extracted.

Value

list of signature specific features or binary matrices for all features

Examples

data("leukemia")
nmf_exp <- run_NMF_tensor(leukemia$matrix, ranks = 3,
                             method = "NMF",
                             n_initializations = 2,
                             extract_features = TRUE)
SignatureSpecificFeatures(nmf_exp)
SignatureSpecificFeatures(nmf_exp, k = 3)
SignatureSpecificFeatures(nmf_exp, k = 3, return_all_features = TRUE)
## Not run: 
# For ButchR_NMF objects:
SignatureSpecificFeatures(nmf_exp)
lapply(SignatureSpecificFeatures(nmf_exp), function(x) sapply(x, length))
SignatureSpecificFeatures(nmf_exp, k = 3)
SignatureSpecificFeatures(nmf_exp, k = 3, return_all_features = TRUE)

## End(Not run)
## Not run: 
# For ButchR_integrativeNMF objects:
SignatureSpecificFeatures(inmf_exp)
lapply(SignatureSpecificFeatures(inmf_exp), function(view){
  sapply(view, function(x) sapply(x, length))
} )
lapply(SignatureSpecificFeatures(inmf_exp, k = 3), function(view){
  sapply(view, length)
})
SignatureSpecificFeatures(inmf_exp, k = 3, return_all_features = TRUE)
SignatureSpecificFeatures(inmf_exp, k = 3,
                          return_all_features = TRUE,
                          view_id = "atac")
SignatureSpecificFeatures(inmf_exp,
                          return_all_features = TRUE,
                          view_id = "atac")

## End(Not run)

## Not run: 
# For ButchR_joinNMF objects:
SignatureSpecificFeatures(jnmf_exp)
SignatureSpecificFeatures(jnmf_exp)
lapply(SignatureSpecificFeatures(jnmf_exp), function(view){
  sapply(view, function(x) sapply(x, length))
})
lapply(SignatureSpecificFeatures(jnmf_exp, k = 3), function(view){
  sapply(view, length)
})
SignatureSpecificFeatures(jnmf_exp, k = 3, return_all_features = TRUE)
SignatureSpecificFeatures(jnmf_exp, k = 3,
                          return_all_features = TRUE,
                          view_id = "atac")
SignatureSpecificFeatures(jnmf_exp,
                          return_all_features = TRUE,
                          view_id = "atac")

## End(Not run)

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