Man pages for BIMIB-DISCo/TRONCO
TRONCO, an R package for TRanslational ONCOlogy
| aCML | Atypical chronic myeloid leukemia dataset |
| AND | AND |
| annotate.description | annotate.description |
| annotate.stages | annotate.stages |
| as.adj.matrix | as.adj.matrix |
| as.alterations | as.alterations |
| as.bootstrap.scores | as.bootstrap.scores |
| as.colors | as.colors |
| as.conditional.probs | as.conditional.probs |
| as.confidence | as.confidence |
| as.description | as.description |
| as.events | as.events |
| as.events.in.patterns | as.events.in.patterns |
| as.events.in.sample | as.events.in.sample |
| as.gene | as.gene |
| as.genes | as.genes |
| as.genes.in.patterns | as.genes.in.patterns |
| as.genotypes | as.genotypes |
| as.hypotheses | as.hypotheses |
| as.joint.probs | as.joint.probs |
| as.kfold.eloss | as.kfold.eloss |
| as.kfold.posterr | as.kfold.posterr |
| as.kfold.prederr | as.kfold.prederr |
| as.marginal.probs | as.marginal.probs |
| as.models | as.models |
| as.parameters | as.parameters |
| as.pathway | as.pathway |
| as.patterns | as.patterns |
| as.samples | as.samples |
| as.selective.advantage.relations | as.selective.advantage.relations |
| as.stages | as.stages |
| as.types | as.types |
| as.types.in.patterns | as.types.in.patterns |
| change.color | change.color |
| consolidate.data | consolidate.data |
| crc_gistic | GISTIC example data |
| crc_maf | MAF example data |
| crc_plain | Plain mutation dataset |
| delete.event | delete.event |
| delete.gene | delete.gene |
| delete.hypothesis | delete.hypothesis |
| delete.model | delete.model |
| delete.pattern | delete.pattern |
| delete.samples | delete.samples |
| delete.type | delete.type |
| duplicates | duplicates |
| ebind | ebind |
| enforce.numeric | enforce.numeric |
| enforce.string | enforce.string |
| events.selection | events.selection |
| export.graphml | export.graphml |
| export.mutex | export,mutex |
| export.nbs.input | export.nbs.input |
| extract.MAF.HuGO.Entrez.map | extract.MAF.HuGO.Entrez.map |
| genes.table.report | genes.table.report |
| has.duplicates | has.duplicates |
| has.model | has.model |
| has.stages | has stages |
| hypothesis.add | hypothesis add |
| hypothesis.add.group | hypothesis add group |
| hypothesis.add.homologous | hypothesis.add.homologous |
| import.genotypes | import.genotypes |
| import.GISTIC | import.GISTIC |
| import.MAF | import.MAF |
| import.model | import.model |
| import.mutex.groups | import.mutex.groups |
| intersect.datasets | intersect.datasets |
| is.compliant | is.compliant |
| join.events | join.events |
| join.types | join.types |
| keysToNames | keysToNames |
| maf | MAF example data |
| muts | Simple mutation dataset |
| nameToKey | nameToKey |
| nevents | nevents |
| ngenes | ngenes |
| nhypotheses | Return the number of hypotheses in the dataset |
| npatterns | Return the number of patterns in the dataset |
| nsamples | nsamples |
| ntypes | ntypes |
| oncoprint | oncoprint |
| oncoprint.cbio | oncoprint.cbio |
| OR | OR |
| order.frequency | order.frequency |
| pathway.visualization | pathway.visualization |
| pheatmap | A function to draw clustered heatmaps. |
| rank.recurrents | rank.recurrents |
| rename.gene | rename.gene |
| rename.type | rename.type |
| samples.selection | samples.selection |
| sbind | sbind |
| ssplit | ssplit |
| stage | Stage information for test_dataset |
| TCGA.map.clinical.data | TCGA.map.clinical.data |
| TCGA.multiple.samples | TCGA.multiple.samples |
| TCGA.remove.multiple.samples | TCGA.remove.multiple.samples |
| TCGA.shorten.barcodes | TCGA.shorten.barcodes |
| test_dataset | A complete dataset with hypotheses |
| test_dataset_no_hypos | A complete dataset |
| test_model | A complete dataset with a reconstructed model |
| test_model_kfold | A complete dataset with a reconstructed model and... |
| trim | trim |
| tronco.bootstrap | tronco bootstrap |
| tronco.caprese | tronco caprese |
| tronco.capri | tronco capri |
| tronco.chowliu | Tronco Chow Liu |
| tronco.edmonds | Tronco Edmonds |
| tronco.gabow | Tronco Gabow |
| tronco.kfold.eloss | tronco.kfold.eloss |
| tronco.kfold.posterr | tronco.kfold.posterr. For details and examples regarding the... |
| tronco.kfold.prederr | tronco.kfold.prederr |
| tronco.pattern.plot | tronco.pattern.plot |
| tronco.plot | tronco.plot |
| tronco.prim | Tronco Prim |
| view | view |
| which.samples | which.samples |
| XOR | XOR |
