# Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

## Documentation for package ‘padma’ version 1.8.0

- 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