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Lung adenocarcinoma from TCGA cohort as SelectSim run object

Source: R/data.R
luad_run_data.Rd

Preprocessed TCGA LUAD data ready to pass directly to selectX().

Usage

data(luad_run_data)

Format

A named list with four elements:

M

A named list containing:

M

A named list of binary alteration matrices (genes x samples), one per alteration type (e.g., missense, truncating).

tmb

A named list of data frames, one per alteration type, each with columns sample (character) and mutation (integer TMB count).

sample.class

Named character vector of sample-type annotations (length = number of samples). Names are sample IDs.

alteration.class

Named character vector of alteration-type annotations (length = number of genes). Names are gene symbols.

Value

A named list containing preprocessed LUAD input data for selectX().

Examples

data(luad_run_data)
names(luad_run_data)
#> [1] "M"                "sample.class"     "alteration.class"
str(luad_run_data, max.level = 1)
#> List of 3
#>  $ M               :List of 2
#>  $ sample.class    : Named chr [1:502] "LUAD" "LUAD" "LUAD" "LUAD" ...
#>   ..- attr(*, "names")= chr [1:502] "TCGA-05-4244-01" "TCGA-05-4249-01" "TCGA-05-4250-01" "TCGA-05-4382-01" ...
#>  $ alteration.class: Named chr [1:396] "MUT" "MUT" "MUT" "MUT" ...
#>   ..- attr(*, "names")= chr [1:396] "AKT1" "ALK" "APC" "AR" ...