Return the genotypes for a certain set of genes and type of events. Input 'x' should be a
TRONCO compliant dataset - see is.compliant. In this case column names are substituted
with events' types.
as.gene(x, genes, types = NA)A matrix, subset of as.genotypes(x) with colnames substituted with events' types.
data(test_dataset)
as.gene(test_dataset, genes = c('EZH2', 'ASXL1'))
#> ins_del EZH2 ins_del ASXL1 missense_point_mutations EZH2
#> patient 1 0 0 0
#> patient 2 0 0 0
#> patient 3 0 0 0
#> patient 4 0 0 0
#> patient 5 0 0 0
#> patient 6 0 0 0
#> patient 7 0 0 0
#> patient 8 0 0 0
#> patient 9 0 1 0
#> patient 10 0 0 0
#> patient 11 0 0 0
#> patient 12 0 0 0
#> patient 13 0 0 0
#> patient 14 0 0 0
#> patient 15 0 0 0
#> patient 16 0 0 0
#> patient 17 0 0 1
#> patient 18 0 0 0
#> patient 19 0 0 0
#> patient 20 0 0 1
#> patient 21 0 1 0
#> patient 22 0 0 0
#> patient 23 0 0 1
#> patient 24 0 1 1
#> patient 25 0 0 0
#> patient 26 0 0 0
#> patient 27 1 1 0
#> patient 28 0 0 0
#> patient 29 0 1 1
#> patient 30 0 0 0
#> patient 31 0 0 0
#> patient 32 0 1 0
#> patient 33 0 0 0
#> patient 34 0 0 0
#> patient 35 0 0 0
#> patient 36 0 0 0
#> patient 37 0 0 0
#> patient 38 0 0 1
#> patient 39 0 1 0
#> patient 40 0 0 0
#> nonsense_point_mutations EZH2 nonsense_point_mutations ASXL1
#> patient 1 0 0
#> patient 2 0 1
#> patient 3 0 0
#> patient 4 0 1
#> patient 5 0 0
#> patient 6 1 0
#> patient 7 0 1
#> patient 8 0 1
#> patient 9 0 0
#> patient 10 0 0
#> patient 11 0 0
#> patient 12 0 0
#> patient 13 0 0
#> patient 14 0 0
#> patient 15 0 0
#> patient 16 0 0
#> patient 17 0 0
#> patient 18 0 0
#> patient 19 0 0
#> patient 20 0 0
#> patient 21 0 0
#> patient 22 0 0
#> patient 23 0 0
#> patient 24 0 0
#> patient 25 0 0
#> patient 26 0 0
#> patient 27 0 0
#> patient 28 0 0
#> patient 29 0 0
#> patient 30 0 0
#> patient 31 0 0
#> patient 32 0 0
#> patient 33 0 0
#> patient 34 0 0
#> patient 35 0 0
#> patient 36 0 0
#> patient 37 0 0
#> patient 38 0 0
#> patient 39 0 0
#> patient 40 0 0