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Convert MultiAssayExperiment to TreatmentResponseExperiment

Source: R/MAE_to_PSet.R
convert_MAE_to_PSet.Rd

This function converts a MultiAssayExperiment generated by gDR into a TreatmentResponseExperiment for use in the PharmacoGx package. The resulting PharmacoSet can be used for pharmacogenomic analysis of drug response.

Usage

convert_MAE_to_PSet(mae, pset_name)

Arguments

mae

A MultiAssayExperiment object generated by gDR.

pset_name

A character string specifying the name of the resulting PharmacoSet object.

Value

A PharmacoSet object.

Examples

# Convert a MultiAssayExperiment object to a PharmacoSet object
m <- 20
n <- 10
rnames <- LETTERS[1:m]
cnames <- letters[1:n]
ref_gr_value <-  matrix(runif(m * n), nrow = m, ncol = n, dimnames = list(rnames, cnames))
se <- SummarizedExperiment::SummarizedExperiment(assays = list(RefGRvalue = ref_gr_value),
                                                 rowData = S4Vectors::DataFrame(rnames),
                                                 colData = S4Vectors::DataFrame(cnames))
mae <- MultiAssayExperiment::MultiAssayExperiment(experiments = list("single-agent" = se))
convert_MAE_to_PSet(mae, "my_pset")
#> <PharmacoSet>
#> Name:  my_pset 
#> Date Created:  Thu Nov  7 10:36:41 2024 
#> Number of samples:  10 
#> Molecular profiles:
#>    A MultiAssayExperiment object of 1 listed
#>    experiment with a user-defined name and respective class.
#>    Containing an ExperimentList class object of length 1:
#>    [1] emptySE: SummarizedExperiment with 0 rows and 10 columns 
#> Treatment response:
#>    <TreatmentResponseExperiment> 
#>   dim:  20 10 
#>   assays(1): RefGRvalue 
#>   rownames(20): A B ... S T 
#>   rowData(2): treatmentid rnames 
#>   colnames(10): a b c ... h i j 
#>   colData(2): sampleid cnames 
#>   metadata(0): none