Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

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Documentation for package ‘padma’ version 1.14.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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