summary: Summarize results from padma

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

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)

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