padmaResults-class {padma} | R 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

[Package padma version 1.0.0 Index]