as.types

Return the types of events for a set of genes which are in 'x', which should be a TRONCO compliant dataset - see is.compliant.

as.types(x, genes = NA)

Arguments

x

A TRONCO compliant dataset.

genes

A list of genes to consider, if NA all genes are used.

Value

A matrix with 1 column annotating stages and rownames as sample IDs.

Examples

data(test_dataset)
as.types(test_dataset)
#> [1] "ins_del"                  "missense_point_mutations"
#> [3] "nonsense_ins_del"         "nonsense_point_mutations"
#> [5] "Pattern"                 
as.types(test_dataset, genes='TET2')
#> [1] "ins_del"                  "missense_point_mutations"
#> [3] "nonsense_point_mutations"