Multi-omic Pathway Analysis of Cells

Documentation for package ‘MPAC’ version 1.3.0

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