Man pages for BRL-BCM/CTD
CTD method for “connecting the dots” in weighted graphs

data.HMDBtoKEGGConvert HMDB IDs to KEGG compound IDs.
data.LabeltoKEGGConvert compound names to KEGG compound IDs.
data.surrogateProfilesSurrogate profiles
graph.diffuseP1Diffuse Probability P1 from a starting node.
graph.diffuseP1MovieMake a movie of the diffusion of probability, P1, from a...
graph.naivePruningPruning edges from disease differential network that also...
mle.blowoutSimModule that best explains the patient similarity assigned...
mle.getEncodingLengthMinimum encoding length (MLE)
mle.getMinPtDistanceMetabolite set enrichment analysis (MSEA) using pathway...
mle.getPtSimPatient similarity using mutual information MLE metric of...
mle.kraftMcMillanApply the Kraft-McMillian Inequality using a specific...
multiNode.getNodeRanksGenerate the "adaptive walk" node rankings, starting from a...
multiNode.getNodeRanksMovieCapture the movement of the adaptive walk of the diffusion...
multiNode.getPtBSbyKGenerate patient-specific bitstrings from adaptive network...
pathway.ListMaps_metabolonGet All Metabolites In Metabolon's Pathway Knowledgebase
pathway.ListMetabolites_metabolonGet All Metabolites In Metabolon's Pathway Knowledgebase
plot.getPathwayIgraphplot.getPathwayIgraph
plot.hmSimGenerate heatmap plot of patient similarity matrix.
plot.knnSimVisualize the confusion matrix using nearest neighbor as...
plot.mdsSimView patient clusters using multi-dimensional scaling.
plot.pathwayMapGenerate pathway map with patient perturbation data...
singleNode.getNodeRanksMovieCapture the movement of the fixed, single-node walk of the...
singleNode.getNodeRanksNGenerate the fixed , single-node diffusion node rankings,...
singleNode.getPtBSbyKGenerate patient-specific bitstrings from the fixed,...
stats.entropyFunctionEntropy of a bit-string
stats.fishersMethodFisher's Combined P-value
stats.getMSEA_MetabolonMetabolite set enrichment analysis (MSEA) using pathway...
stats.getORA_MetabolonMetabolite set enrichment analysis (MSEA) (using a...
BRL-BCM/CTD documentation built on Nov. 11, 2019, 10:03 p.m.