predict_exposure {musicatk} | R Documentation |
Exposures for samples will be predicted using an existing set
of signatures stored in a musica_result
object.
Algorithms available for prediction include a modify version of "lda"
,
"decompTumor2Sig"
, and "deconstructSigs"
.
predict_exposure( musica, g, table_name, signature_res, algorithm = c("lda", "decompTumor2Sig", "deconstructSigs"), signatures_to_use = seq_len(ncol(signatures(signature_res))), verbose = FALSE )
musica |
A |
g |
A BSgenome object indicating which genome
reference the variants and their coordinates were derived from. Only used
if |
table_name |
Name of table used for posterior prediction. Must match the table type used to generate the prediction signatures |
signature_res |
Signatures used to predict exposures for the samples
|
algorithm |
Algorithm to use for prediction of exposures. One of
|
signatures_to_use |
Which signatures in the |
verbose |
If |
Returns a A musica_result
object containing
signatures given by the signature_res
parameter and exposures
predicted from these signatures.
data(musica) data(cosmic_v2_sigs) g <- select_genome("19") build_standard_table(musica, g, "SBS96", overwrite = TRUE) result <- predict_exposure(musica = musica, table_name = "SBS96", signature_res = cosmic_v2_sigs, algorithm = "lda") # Predict using LDA-like algorithm with seed set to 1 set.seed(1) predict_exposure(musica = musica, table_name = "SBS96", signature_res = cosmic_v2_sigs, algorithm = "lda")