annotate.stages

Annotate stage information on the selected dataset

annotate.stages(x, stages, match.TCGA.patients = FALSE)

Arguments

x

A TRONCO compliant dataset.

stages

A list of stages. Rownames must match samples list of x

match.TCGA.patients

Match using TCGA notations (only first 12 characters)

Value

A TRONCO compliant dataset.

Examples

data(test_dataset)
data(stage)
test_dataset = annotate.stages(test_dataset, stage)
#> Warning: 6  missing stages were added as NA.
as.stages(test_dataset)
#>                stage
#> patient 1   Stage II
#> patient 2    Stage I
#> patient 3   Stage II
#> patient 4    Stage I
#> patient 5    Stage I
#> patient 6   Stage II
#> patient 7    Stage I
#> patient 8    Stage I
#> patient 9       <NA>
#> patient 10   Stage I
#> patient 11 Stage III
#> patient 12   Stage I
#> patient 13      <NA>
#> patient 14   Stage I
#> patient 15   Stage I
#> patient 16  Stage II
#> patient 17   Stage I
#> patient 18 Stage III
#> patient 19   Stage I
#> patient 20  Stage II
#> patient 21   Stage I
#> patient 22 Stage III
#> patient 23      <NA>
#> patient 24   Stage I
#> patient 25  Stage II
#> patient 26  Stage II
#> patient 27      <NA>
#> patient 28   Stage I
#> patient 29  Stage II
#> patient 30 Stage III
#> patient 31 Stage III
#> patient 32   Stage I
#> patient 33   Stage I
#> patient 34  Stage II
#> patient 35  Stage II
#> patient 36 Stage III
#> patient 37   Stage I
#> patient 38      <NA>
#> patient 39 Stage III
#> patient 40      <NA>