Function to remove the contribution of a SuperSig

Source: R/partial_signature.R

Remove the contribution of a SuperSig from the data and return the data.

partial_signature(data, object)

Arguments

data

a data frame of mutations containing columns for sample_id, age, IndVar, and the 96 trinucleotide mutations (see vignette for details)
object

an object of class SuperSig

Value

predict_signature returns the original data frame with the contribution of a supervised signature removed

Examples


head(example_dt) # use example data from package

#>   sample_id age chromosome  position ref alt
#> 1         1  50       chr1  94447621   G   C
#> 2         1  50       chr2 202005395   A   C
#> 3         1  50       chr7  20784978   T   A
#> 4         1  50       chr7  87179255   C   G
#> 5         1  50      chr19   1059712   G   T
#> 6         2  55       chr1  76226977   T   C
input_dt <- make_matrix(example_dt) # convert to correct format
input_dt$IndVar <- c(1, 1, 1, 0, 0) # add IndVar column
supersig <- get_signature(data = input_dt, factor = "Age") # get SuperSig

#> Begin feature engineering...
#> Begin cross-validated selection over 4 features and 15 inner folds...
#> ...testing inner fold 1
#> ...testing inner fold 2
#> ...testing inner fold 3
#> ...testing inner fold 4
#> ...testing inner fold 5
#> ...testing inner fold 6
#> ...testing inner fold 7
#> ...testing inner fold 8
#> ...testing inner fold 9
#> ...testing inner fold 10
#> ...testing inner fold 11
#> ...testing inner fold 12
#> ...testing inner fold 13
#> ...testing inner fold 14
#> ...testing inner fold 15
partial_signature(data = input_dt, object = supersig)

#> # A tibble: 5 x 99
#>   sample_id   AGE `A[T>G]T` `C[T>A]A` `G[C>A]A` `G[C>G]G` `G[C>G]T` `A[C>G]T`
#>       <dbl> <dbl>     <dbl>     <dbl>     <dbl>     <dbl>     <dbl>     <dbl>
#> 1         1    50         0         1         1         0         0         0
#> 2         2    55         0         0         0         0         0         1
#> 3         3    72         0         1         0         0         0         0
#> 4         4    53         0         0         0         0         0         1
#> 5         5    48         0         1         1         0         0         0
#> # … with 91 more variables: C[C>A]T <dbl>, C[T>C]G <dbl>, T[C>A]C <dbl>,
#> #   T[C>A]T <dbl>, A[T>C]C <dbl>, C[T>C]C <dbl>, T[T>A]C <dbl>, C[C>G]G <dbl>,
#> #   G[C>T]A <dbl>, A[C>A]T <dbl>, C[C>A]C <dbl>, G[T>G]T <dbl>, C[C>T]C <dbl>,
#> #   T[C>T]C <dbl>, A[C>T]C <dbl>, G[C>T]C <dbl>, C[C>T]T <dbl>, T[C>T]T <dbl>,
#> #   A[C>T]T <dbl>, G[C>T]T <dbl>, C[C>T]A <dbl>, T[C>T]A <dbl>, A[C>T]A <dbl>,
#> #   C[C>T]G <dbl>, T[C>T]G <dbl>, A[C>T]G <dbl>, G[C>T]G <dbl>, A[C>A]C <dbl>,
#> #   G[C>A]C <dbl>, G[C>A]T <dbl>, C[C>A]A <dbl>, T[C>A]A <dbl>, A[C>A]A <dbl>,
#> #   C[C>A]G <dbl>, T[C>A]G <dbl>, A[C>A]G <dbl>, G[C>A]G <dbl>, C[C>G]C <dbl>,
#> #   T[C>G]C <dbl>, A[C>G]C <dbl>, G[C>G]C <dbl>, C[C>G]T <dbl>, T[C>G]T <dbl>,
#> #   C[C>G]A <dbl>, T[C>G]A <dbl>, A[C>G]A <dbl>, G[C>G]A <dbl>, T[C>G]G <dbl>,
#> #   A[C>G]G <dbl>, T[T>C]C <dbl>, G[T>C]C <dbl>, C[T>C]T <dbl>, T[T>C]T <dbl>,
#> #   A[T>C]T <dbl>, G[T>C]T <dbl>, C[T>C]A <dbl>, T[T>C]A <dbl>, A[T>C]A <dbl>,
#> #   G[T>C]A <dbl>, T[T>C]G <dbl>, A[T>C]G <dbl>, G[T>C]G <dbl>, C[T>A]C <dbl>,
#> #   A[T>A]C <dbl>, G[T>A]C <dbl>, C[T>A]T <dbl>, T[T>A]T <dbl>, A[T>A]T <dbl>,
#> #   G[T>A]T <dbl>, T[T>A]A <dbl>, A[T>A]A <dbl>, G[T>A]A <dbl>, C[T>A]G <dbl>,
#> #   T[T>A]G <dbl>, A[T>A]G <dbl>, G[T>A]G <dbl>, C[T>G]C <dbl>, T[T>G]C <dbl>,
#> #   A[T>G]C <dbl>, G[T>G]C <dbl>, C[T>G]T <dbl>, T[T>G]T <dbl>, C[T>G]A <dbl>,
#> #   T[T>G]A <dbl>, A[T>G]A <dbl>, G[T>G]A <dbl>, C[T>G]G <dbl>, T[T>G]G <dbl>,
#> #   A[T>G]G <dbl>, G[T>G]G <dbl>, IndVar <dbl>