R: Multi-omic Pathway Analysis of Cells

# Multi-omic Pathway Analysis of Cells

## Documentation for package ‘MPAC’ version 1.7.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

clSamp | Cluster samples by pathway over-representation
colPermIPL | Collect Inferred Pathway Levels (IPLs) from PARADIGM runs on permuted data
colRealIPL | Collect Inferred Pathway Levels (IPLs) from PARADIGM runs on real data
conMtf | Find consensus pathway motifs from a list of pathways
fltByPerm | Filter IPLs from real data by distribution from permuted data
getSignifOvrOnCl | Get significantly over-represented gene sets for clustered samples
ovrGMT | Calculate over-representation of gene sets in each sample by genes from sample's largest sub-pathway
pltConMtf | Plot consensus pathway submodules
pltMtfPrtIPL | Plot a heatmap of IPLs on proteins from consensus pathway submodules
pltNeiStt | Plot a heatmap of pathway and omic states of a protein and its pathway neighbors
pltOvrHm | Plot a heatmap of over-represented gene sets for clustered samples
pltSttKM | Plot a Kaplan-Meier curve for samples stratified by given protein(s)' pathway states
ppCnInp | Prepare input copy-number (CN) alteration data to run PARADIGM
ppPermInp | Permute input genomic state data between genes in the same sample
ppRealInp | Prepare input copy-number (CN) alteration and RNA data to run PARADIGM
ppRnaInp | Prepare input RNA data to run PARADIGM
ppRunPrd | Prepare required files to run PARADIGM
runPermPrd | Run PARADIGM on permuted data
runPrd | Run PARADIGM on multi-omic data
subNtw | Subset pathways by IPL results