padmaResults: padmaResults object and constructor

View source: R/aaa-AllClasses.R

padmaResults-classR Documentation

padmaResults object and constructor

Description

padmaResults is a subclass of RangedSummarizedExperiment, used to store the individualized pathway deviation scores as well as some additional information useful about the pathway name (pathway_name), the gene-level contributions to each deviation score (pathway_gene_deviation), a full set of outputs related to the MFA (MFA_results, and the number of genes used in the analysis as well as the names of those for which data imputation or filtering was required (ngenes, imputed_genes, and removed_genes, respectively).

Usage

padmaResults(
  SummarizedExperiment,
  pathway_name = NULL,
  pathway_gene_deviation = NULL,
  MFA_results = NULL,
  ngenes = NULL,
  imputed_genes = NULL,
  removed_genes = NULL
)

Arguments

SummarizedExperiment

a RangedSummarizedExperiment of padma results

pathway_name

The name of the pathway, if applicable

pathway_gene_deviation

Per-gene contributions to each individualized pathway deviation score

MFA_results

List of all detailed results from the MFA

ngenes

Number of genes used in the pathway deviation score calculation

imputed_genes

Names of genes, per omic, for which data imputation was used to replace missing values

removed_genes

Names of genes, per omic, which were filtered from the analysis due to low variation

Details

This constructor function would not typically be used by 'end users'. This simple class extends the RangedSummarizedExperiment class of the SummarizedExperiment package to allow other packages to write methods for results objects from the padma package. It is used by padmaRun to wrap up the results table.

Value

a padmaResults object


andreamrau/padma documentation built on June 15, 2024, 8:39 a.m.