summary,padmaResults-method | R Documentation |
A function to summarize the pathway deviation results from padma
,
using the quantiles of the calculated multi-omic pathway deviation scores.
## S4 method for signature 'padmaResults' summary(object, ...)
object |
An object of class |
... |
Additional arguments |
Summary of the padmaResults
object.
Andrea Rau
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.
padma
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)
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