A C D E G H I K M N O P R S T W X
TRONCO-package | TRONCO is a R package which collects algorithms to infer progression models from Bernoulli 0/1 profiles of genomic alterations across a tumor sample. Such profiles are usually visualized as a binary input matrix where each row represents a patient’s sample (e.g., the result of a sequenced tumor biopsy), and each column an event relevant to the progression (a certain type of somatic mutation, a focal or higher-level chromosomal copy number alteration, etc.); a 0/1 value models the absence/presence of that alteration in the sample. In this version of TRONCO such profiles can be readily imported by boolean matrices and MAF or GISTIC files. The package provides various functions to editing, visualize and subset such data, as well as functions to query the cBioPortal for cancer genomics. In the current version, TRONCO provides parallel implementations of CAPRESE [PLoS ONE 9(12): e115570] and CAPRI [Bioinformatics, doi:10.1093/bioinformatics/btv296] algorithms to infer progression models arranged as trees or general direct acyclic graphs. Bootstrap procedures to assess the non-prametric and statistical confidence of the inferred models are also provided. The package comes with example data available, which include the dataset of Atypical Chronic Myeloid Leukemia samples by Piazza et al., Nat. Genet., 45 (2013). |
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.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.events.test | as events matrix |
as.gene | as.gene |
as.genes | as.genes |
as.genes.in.patterns | as.genes.in.patterns |
as.genotypes | as.genotypes |
as.genotypes.test | as genotypes matrix |
as.hypotheses | as.hypotheses |
as.joint.probs | as.joint.probs |
as.marginal.probs | as.marginal.probs |
as.models | as.models |
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.stages.test | as stages matrix |
as.types | as.types |
as.types.in.patterns | as.types.in.patterns |
cbio.query | cbio.query |
change.color | change.color |
consolidate.data | consolidate.data |
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.mutex | export,mutex |
export.nbs.input | export.nbs.input |
extract.MAF.HuGO.Entrez.map | extract.MAF.HuGO.Entrez.map |
genes.table.plot | genes.table.plot |
genes.table.report | genes.table.report |
gistic | GISTIC example data |
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.mutex.groups | import.mutex.groups |
intersect.datasets | intersect.datasets |
is.compliant | is.compliant |
keysToNames | keysToNames |
maf | MAF example data |
merge.events | merge.events |
merge.types | merge.types |
muts | Simple mutation dataset |
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 |
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 |
show | show |
sort.by.frequency | sort.by.frequency |
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 |
trim | trim |
TRONCO | TRONCO is a R package which collects algorithms to infer progression models from Bernoulli 0/1 profiles of genomic alterations across a tumor sample. Such profiles are usually visualized as a binary input matrix where each row represents a patient’s sample (e.g., the result of a sequenced tumor biopsy), and each column an event relevant to the progression (a certain type of somatic mutation, a focal or higher-level chromosomal copy number alteration, etc.); a 0/1 value models the absence/presence of that alteration in the sample. In this version of TRONCO such profiles can be readily imported by boolean matrices and MAF or GISTIC files. The package provides various functions to editing, visualize and subset such data, as well as functions to query the cBioPortal for cancer genomics. In the current version, TRONCO provides parallel implementations of CAPRESE [PLoS ONE 9(12): e115570] and CAPRI [Bioinformatics, doi:10.1093/bioinformatics/btv296] algorithms to infer progression models arranged as trees or general direct acyclic graphs. Bootstrap procedures to assess the non-prametric and statistical confidence of the inferred models are also provided. The package comes with example data available, which include the dataset of Atypical Chronic Myeloid Leukemia samples by Piazza et al., Nat. Genet., 45 (2013). |
tronco.bootstrap | tronco bootstrap |
tronco.caprese | tronco caprese |
tronco.capri | tronco capri |
tronco.plot | tronco.plot |
which.samples | which.samples |
XOR | XOR |