Multi-omic Pathway Analysis of Cells


[Up] [Top]

Documentation for package ‘MPAC’ version 1.1.5

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
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
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