Skip to contents

Retrieve exposures from a result_model, result_collection, or musica object

Source: R/class_result_model.R
exposures.Rd

The exposure matrix contains estimated amount of each signature for each sample. Rows correspond to each signature and columns correspond to each sample.

Usage

exposures(x, ...)

# S4 method for class 'musica'
exposures(x, result, modality, model_id)

# S4 method for class 'result_collection'
exposures(x, modality, model_id)

# S4 method for class 'result_model'
exposures(x)

exposures(x, ...) <- value

# S4 method for class 'musica,matrix'
exposures(x, result, modality, model_id) <- value

# S4 method for class 'result_collection,matrix'
exposures(x, modality, model_id) <- value

# S4 method for class 'result_model,matrix'
exposures(x) <- value

Arguments

x

A musica, result_collection, or result_model object generated by a mutational discovery or prediction tool.

...

Other inputs

result

Name of result from result_list to assign the exposures. Used when result is a musica object.

modality

Modality to assign the exposures. Used when result is a musica or result_collection object.

model_id

Model identifier to assign the exposures. Used when result is a musica or result_collection object.

value

A matrix of samples by signature exposures

Value

A matrix of exposures

Examples

data(res)
exposures(res, "result", "SBS96", "res")
#>            TCGA-56-7582-01A-11D-2042-08 TCGA-77-7335-01A-11D-2042-08
#> Signature1                   0.09060907                 175.47415750
#> Signature2                 191.81878100                  98.43519276
#> Signature3                   0.09060993                   0.09064974
#>            TCGA-94-7557-01A-11D-2122-08 TCGA-97-7938-01A-11D-2167-08
#> Signature1                     64.48884                 116.81894638
#> Signature2                     38.41289                   0.09052656
#> Signature3                     14.09827                   0.09052706
#>            TCGA-EE-A3J5-06A-11D-A20D-08 TCGA-ER-A197-06A-32D-A197-08
#> Signature1                    0.0905308                   6.89236265
#> Signature2                    0.0905325                   4.01908283
#> Signature3                  121.8189367                   0.08855452
#>            TCGA-ER-A19O-06A-11D-A197-08
#> Signature1                   0.09025138
#> Signature2                   0.09025280
#> Signature3                  50.81949582
data(res)
exposures(res, "result", "SBS96", "res") <- matrix()