This function extracts and merges exposure variables from colData with selected features from omics datasets
in a MultiAssayExperiment object. Optionally applies log2 transformation to omics data and restricts features based on a variable map.
Usage
extract_omics_exposure_df(expomicset, variable_map, log2_trans = TRUE)
Arguments
- expomicset
A MultiAssayExperiment object containing omics and exposure data.
- variable_map
A data frame with columns "variable" and "exp_name", indicating which variables belong to each omics or exposure domain.
- log2_trans
Logical; whether to log2-transform omics data. Default is TRUE.
Value
A data frame where rows correspond to samples, and columns contain exposure variables and log2-transformed omics features.
Columns from different omics types are disambiguated using prefixes.
Details
If variable_map is provided, it is used to select variables from both exposures and omics. If not provided, all numeric colData variables
are used as exposures (excluding variables matching ^PC), and all omics features are included.
Examples
if (FALSE) { # \dontrun{
merged_df <- extract_omics_exposure_df(expomicset, variable_map = my_map)
} # }