padmaResults: padmaResults object and constructor

In padma: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

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

padma documentation built on Nov. 8, 2020, 4:56 p.m.