Man pages for jdreyf/PANTS
Pathway analysis via network smoothing

diag_kernelMake diagonal kernel matrix
edgelist2graphTransform a data frame edge list into an 'igraph' graph
ezpermutationsResample sample labels for permutation testing
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
match_matsExpand kernel to match features in object and pathway matrix
mat_powCalculate power of a matrix
neighbor_nmsGet names of nodes' neighbors
opt_binom_nFind minimal binomial N that ensures 'ezpermutations' obtains...
pantsPathway analysis via network smoothing (Pants)
p_ecdfEstimate p-value from simulations
plot_pwyPlot network diagram for a pathway
sapply_by_ncoresSapply by number of cores
score_featuresScore features using ezlimma and score_fcn
select_ntop_per_pwySelect top drivers for a pathway
sif2edgelistClean Pathway Commons SIF file
sim_pantsSimulate 'pants' to estimate size & power
sim_pants_mediationSimulate 'pants' with mediation to estimate size & power
SMPDB2GmatTransform SMPDB protein and/or metabolite pathway data frames...
subset_gmatSubset pathway inclusion matrix based on size
write_pants_xlWrite Excel XLSX file with links to CSVs
jdreyf/PANTS documentation built on July 18, 2019, 10:12 a.m.