RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes


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Documentation for package ‘RESOLVE’ version 1.9.1

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associationAlterations associationAlterations
associationPrognosis associationPrognosis
associationSignatures associationSignatures
association_mutations List providing mutations as binary variables and signatures assignments for 656 breast cancer patients
association_survival List providing clinical data and signatures assignments for 359 pancreatic cancer patients
background Germline replication error
background2 COSMIC replication error
cn_example_reduced A reduced version of the copy number data for 5 TCGA samples in the format compatible with the import function
getCNCounts getCNCounts
getIDCounts getIDCounts
getMNVCounts getMNVCounts
getSBSCounts getSBSCounts
groupsCNPlot groupsCNPlot
groupsCXPlot groupsCXPlot
groupsIDPlot groupsIDPlot
groupsMNVPlot groupsMNVPlot
groupsSBSPlot groupsSBSPlot
id_example_reduced A reduced version of the indel data for 3 samples in the format compatible with the import function
patients Point mutations for 560 breast tumors
patientsCNPlot patientsCNPlot
patientsCXPlot patientsCXPlot
patientsIDPlot patientsIDPlot
patientsMNVPlot patientsMNVPlot
patientsSBSPlot patientsSBSPlot
plot_data_examples List data structure to run examples
sbs_assignments SBS assignments for 560 breast tumors
signaturesAssignment signaturesAssignment
signaturesClustering signaturesClustering
signaturesCNPlot signaturesCNPlot
signaturesCV signaturesCV
signaturesCXPlot signaturesCXPlot
signaturesDecomposition signaturesDecomposition
signaturesIDPlot signaturesIDPlot
signaturesMNVPlot signaturesMNVPlot
signaturesSBSPlot signaturesSBSPlot
signaturesSignificance signaturesSignificance
ssm560_reduced A reduced version of the point mutations for 560 breast tumors in the format compatible with the import function