API for TRONCO
TRONCO, an R package for TRanslational ONCOlogy
| Global functions | |
|---|---|
| .onLoad | Source code |
| AND | Man page Source code |
| OR | Man page Source code |
| TCGA.map.clinical.data | Man page Source code |
| TCGA.multiple.samples | Man page Source code |
| TCGA.remove.multiple.samples | Man page Source code |
| TCGA.shorten.barcodes | Man page Source code |
| XOR | Man page Source code |
| aCML | Man page |
| annotate.description | Man page Source code |
| annotate.stages | Man page Source code |
| as.adj.matrix | Man page Source code |
| as.alterations | Man page Source code |
| as.bnlearn.network | Source code |
| as.bootstrap.scores | Man page Source code |
| as.categorical.dataset | Source code |
| as.colors | Man page Source code |
| as.conditional.probs | Man page Source code |
| as.confidence | Man page Source code |
| as.description | Man page Source code |
| as.error.rates | Source code |
| as.events | Man page Source code |
| as.events.in.patterns | Man page Source code |
| as.events.in.sample | Man page Source code |
| as.gene | Man page Source code |
| as.genes | Man page Source code |
| as.genes.in.patterns | Man page Source code |
| as.genotypes | Man page Source code |
| as.hypotheses | Man page Source code |
| as.joint.probs | Man page Source code |
| as.kfold.eloss | Man page Source code |
| as.kfold.posterr | Man page Source code |
| as.kfold.prederr | Man page Source code |
| as.marginal.probs | Man page Source code |
| as.models | Man page Source code |
| as.parameters | Man page Source code |
| as.parents.pos | Source code |
| as.pathway | Man page Source code |
| as.patterns | Man page Source code |
| as.samples | Man page Source code |
| as.selective.advantage.relations | Man page Source code |
| as.stages | Man page Source code |
| as.types | Man page Source code |
| as.types.in.patterns | Man page Source code |
| aux.log | Source code |
| bootstrap | Source code |
| caprese.fit | Source code |
| capri.fit | Source code |
| cbio.query | Man page Source code |
| change.color | Man page Source code |
| check.dataset | Source code |
| chow.liu.fit | Source code |
| cluster.sensitivity | Source code |
| cluster_mat | Source code |
| compute.edmonds.score | Source code |
| consolidate.data | Man page Source code |
| convert_annotations | Source code |
| crc_gistic | Man page |
| crc_maf | Man page |
| crc_plain | Man page |
| create.model | Source code |
| decimal.to.binary.dag | Source code |
| delete.event | Man page Source code |
| delete.gene | Man page Source code |
| delete.hypothesis | Man page Source code |
| delete.model | Man page Source code |
| delete.pattern | Man page Source code |
| delete.samples | Man page Source code |
| delete.type | Man page Source code |
| draw_annotation_legend | Source code |
| draw_annotation_names | Source code |
| draw_annotations | Source code |
| draw_colnames | Source code |
| draw_dendrogram | Source code |
| draw_legend | Source code |
| draw_main | Source code |
| draw_matrix | Source code |
| draw_rownames | Source code |
| duplicates | Man page Source code |
| ebind | Man page Source code |
| edmonds.fit | Source code |
| emap | Source code |
| enforce.numeric | Man page Source code |
| enforce.string | Man page Source code |
| estimate.theoretical.probs | Source code |
| events.selection | Man page Source code |
| export.graphml | Man page Source code |
| export.mutex | Man page Source code |
| export.nbs.input | Man page Source code |
| extract.MAF.HuGO.Entrez.map | Man page Source code |
| find.best.subtree | Source code |
| find_coordinates | Source code |
| find_gaps | Source code |
| gabow.fit | Source code |
| generate_annotation_colours | Source code |
| generate_breaks | Source code |
| genes.table.report | Man page Source code |
| get.best.scored.tree | Source code |
| get.bootstrapped.scores | Source code |
| get.dag.scores | Source code |
| get.lifted.pattern | Source code |
| get.prima.facie.causes.do.boot | Source code |
| get.prima.facie.causes.no.boot | Source code |
| get.prima.facie.parents.do.boot | Source code |
| get.prima.facie.parents.no.boot | Source code |
| get.tree.parents | Source code |
| get.tree.scores | Source code |
| has.duplicates | Man page Source code |
| has.model | Man page Source code |
| has.stages | Man page Source code |
| heatmap_motor | Source code |
| hypotheses.expansion | Source code |
| hypothesis.add | Man page Source code |
| hypothesis.add.group | Man page Source code |
| hypothesis.add.homologous | Man page Source code |
| hypothesis.adj.matrix | Source code |
| hypothesis.lifted.effects | Source code |
| import.GISTIC | Man page Source code |
| import.MAF | Man page Source code |
| import.genotypes | Man page Source code |
| import.model | Man page Source code |
| import.mutex.groups | Man page Source code |
| intersect.datasets | Man page Source code |
| is.compliant | Man page Source code |
| is.events.list | Source code |
| is.logic.node | Source code |
| is.logic.node.down | Source code |
| is.logic.node.up | Source code |
| is.model | Source code |
| join.events | Man page Source code |
| join.types | Man page Source code |
| keysToNames | Man page Source code |
| kmeans_pheatmap | Source code |
| lo | Source code |
| lregfit | Source code |
| maf | Man page |
| muts | Man page |
| nameToKey | Man page Source code |
| nevents | Man page Source code |
| ngenes | Man page Source code |
| nhypotheses | Man page Source code |
| npatterns | Man page Source code |
| nsamples | Man page Source code |
| ntypes | Man page Source code |
| oncoprint | Man page Source code |
| oncoprint.cbio | Man page Source code |
| order.frequency | Man page Source code |
| pairwise.fisher.test | Source code |
| pathway.visualization | Man page Source code |
| perform.likelihood.fit.capri | Source code |
| perform.likelihood.fit.chow.liu | Source code |
| perform.likelihood.fit.edmonds | Source code |
| perform.likelihood.fit.gabow | Source code |
| perform.likelihood.fit.prim | Source code |
| pheatmap | Man page Source code |
| prim.fit | Source code |
| rank.recurrents | Man page Source code |
| remove.caprese.loops | Source code |
| remove.cycles | Source code |
| rename.gene | Man page Source code |
| rename.reconstruction.fields | Source code |
| rename.type | Man page Source code |
| sample.RColorBrewer.colors | Source code |
| samples.selection | Man page Source code |
| sbind | Man page Source code |
| scale_colours | Source code |
| scale_mat | Source code |
| scale_rows | Source code |
| scale_vec_colours | Source code |
| ssplit | Man page Source code |
| stage | Man page |
| test_dataset | Man page |
| test_dataset_no_hypos | Man page |
| test_model | Man page |
| test_model_kfold | Man page |
| trim | Man page Source code |
| tronco.bootstrap | Man page Source code |
| tronco.caprese | Man page Source code |
| tronco.capri | Man page Source code |
| tronco.chowliu | Man page Source code |
| tronco.edmonds | Man page Source code |
| tronco.gabow | Man page Source code |
| tronco.kfold.eloss | Man page Source code |
| tronco.kfold.posterr | Man page Source code |
| tronco.kfold.prederr | Man page Source code |
| tronco.pattern.plot | Man page Source code |
| tronco.plot | Man page Source code |
| tronco.prim | Man page Source code |
| tsplit | Source code |
| verify.constraints.probs | Source code |
| verify.parents | Source code |
| verify.probability.raising.do.boot | Source code |
| verify.probability.raising.no.boot | Source code |
| verify.temporal.priority.do.boot | Source code |
| verify.temporal.priority.no.boot | Source code |
| view | Man page Source code |
| vplayout | Source code |
| which.samples | Man page Source code |
