Function to simplify signature representation into interpretable labels for visualization purposes

Source: R/simplify_signature.R

Take a signature representation from SuperSig and group trinucleotides within each feature into interpretable labels, with optional IUPAC labeling from IUPAC_CODE_MAP in the Biostrings package

simplify_signature(object, iupac)

Arguments

object

an object of class SuperSig
iupac

logical value indicating whether to use IUPAC labels (iupac = TRUE) or not (iupac = FALSE)

Value

simplify_signature returns a vector of simplified features and their difference in mean mean rates between exposed and unexposed (or average rate if the factor is "age")

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 = "Smoking")

#> 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
simplify_signature(object = supersig, iupac = FALSE)

#>           C>A           C>T           T>C    [C>G](ACT)    [T>A](CTG) 
#> -1.286204e-04 -1.286204e-04 -1.256126e-04 -1.148120e-04 -1.058889e-04 
#>    [T>G](ACG)   (ACT)[C>G]G   (ATG)[T>A]A   (CTG)[T>G]T 
#> -9.105143e-05 -9.967173e-06 -1.551465e-05 -2.743243e-05 
simplify_signature(object = supersig, iupac = TRUE)

#>           C>A           C>T           T>C        [C>G]H        [T>A]B 
#> -1.286204e-04 -1.286204e-04 -1.256126e-04 -1.148120e-04 -1.058889e-04 
#>        [T>G]V       H[C>G]G       D[T>A]A       B[T>G]T 
#> -9.105143e-05 -9.967173e-06 -1.551465e-05 -2.743243e-05