summary,padmaResults-method {padma} | R Documentation

## Summarize results from padma

### Description

A function to summarize the pathway deviation results from `padma`, using the quantiles of the calculated multi-omic pathway deviation scores.

### Usage

    ## S4 method for signature 'padmaResults'
    summary(object, ...)

### Arguments

`object` | An object of class `'padmaResults'`
`...` | Additional arguments

### Value

Summary of the `padmaResults` object.

### Author(s)

Andrea Rau

### References

Rau, A., Manansala, R., Flister, M. J., Rui, H., Jaffrézic, F., Laloë, D., and Auer, P. L. (2019) Individualized multi-omic pathway deviation scores using multiple factor analysis bioRxiv, https://doi.org/10.1101/827022.

### See Also

`padma`

### Examples

    LUAD_subset <- padma::LUAD_subset
    ## Create MultiAssayExperiment object with LUAD data
    omics_data <-
      list(rnaseq = LUAD_subset$rnaseq,
           methyl = LUAD_subset$methyl,
           mirna = LUAD_subset$mirna,
           cna = LUAD_subset$cna)
    pheno_data <-
      data.frame(LUAD_subset$clinical,
                 row.names = LUAD_subset$clinical$bcr_patient_barcode)
    mae <-
      suppressMessages(
        MultiAssayExperiment::MultiAssayExperiment(
          experiments = omics_data, colData = pheno_data))

    ## Run padma
    run_padma <-
      padma(mae, gene_map = padma::mirtarbase,
            pathway_name = "c2_cp_BIOCARTA_D4GDI_PATHWAY", verbose = FALSE)

    summary(run_padma)

    ## padma plots
    factorMap(run_padma, dim_x = 1, dim_y = 2)
    factorMap(run_padma, dim_x = 1, dim_y = 2,
               partial_id = "TCGA-78-7536")
    omicsContrib(run_padma, max_dim = 10)

[Package padma version 1.0.0 Index]