summary: Summarize results from padma

summary,padmaResults-methodR 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 = as.matrix(LUAD_subset$rnaseq),
       methyl = as.matrix(LUAD_subset$methyl),
       mirna = as.matrix(LUAD_subset$mirna),
       cna = as.matrix(LUAD_subset$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
## Not run: 
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)

## End(Not run)

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