Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis


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Documentation for package ‘padma’ version 1.14.1

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factorMap Plot an MFA factor map for individuals or partial factor map based on padma analysis
imputed_genes Accessors for a padmaResults object.
imputed_genes-method Accessors for a padmaResults object.
LUAD_subset Subset of batch-corrected multi-omic TCGA data in lung adenocarcinoma
MFA_results Accessors for a padmaResults object.
MFA_results-method Accessors for a padmaResults object.
mirtarbase Curated miR-target interaction predictions from miRTarBase
msigdb MSigDB canonical pathways and corresponding gene lists
ngenes Accessors for a padmaResults object.
ngenes-method Accessors for a padmaResults object.
omicsContrib Plot the omics contribution per MFA axis and the overall weighted contribution
padma Calculate individualized deviation scores from multi-omic data
padma-method Calculate individualized deviation scores from multi-omic data
padma-methods Calculate individualized deviation scores from multi-omic data
padmaResults padmaResults object and constructor
padmaResults-class padmaResults object and constructor
padmaRun Calculate individualized deviation scores from multi-omic data
pathway_gene_deviation Accessors for a padmaResults object.
pathway_gene_deviation-method Accessors for a padmaResults object.
pathway_name Accessors for a padmaResults object.
pathway_name-method Accessors for a padmaResults object.
removed_genes Accessors for a padmaResults object.
removed_genes-method Accessors for a padmaResults object.
show Accessors for a padmaResults object.
show-method Accessors for a padmaResults object.
summary Summarize results from padma
summary-method Summarize results from padma
summary-methods Summarize results from padma