Man pages for jdreyf/PANTS
Pathway analysis via network smoothing

color_barPlot colorbar
diag_kernelMake diagonal kernel matrix
edgelist2graphTransform a data frame edge list into an 'igraph' graph
Gmat2gmtTransform analyte-by-pathway matrix into list compatible with...
gmt2GmatTransform list from GMT into feature-by-pathway matrix
graph2kernelTransform an 'igraph' graph into a p-step random walk kernel
map2colorMap values to colors
match_matsExpand kernel to match features in object and pathway matrix
mat_powCalculate power of a matrix
neighbor_nmsGet names of nodes' neighbors
pantsPathway analysis via network smoothing (Pants) testing group...
pants_hitmanPathway Analysis via network smoothing (Pants) testing...
pc9Pathway Commons v9 as an edge-list
p_ecdfEstimate p-value from simulations
plot_pwyPlot network diagram for a pathway
score_featuresScore features using ezlimma and score_fcn
select_ntopSelect top drivers for a pathway
sif2edgelistClean Pathway Commons SIF file
SMPDB2GmatTransform SMPDB protein and/or metabolite pathway data frames...
smpdb_gmatPathway inclusion matrix (Gmat) constructed from SMPDB.
subset_gmatSubset pathway inclusion matrix based on size
write_pants_xlWrite Excel XLSX file with links to CSVs
jdreyf/PANTS documentation built on March 21, 2019, 11:38 p.m.