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Split AlphaVarSet into Subsets by Group

Source: R/10_dataops.R
av_as_subsets.Rd

Splits an AlphaVarSet into a named list of valid AlphaVarSet objects based on the elements of a grouping column.

Usage

av_as_subsets(obj, group_col)

Arguments

obj

An AlphaVarSet object.

group_col

Character. Column name to split by.

Value

A named list of AlphaVarSet objects, one per group element. Each sub-object:

  • Inherits all metadata from the parent.

  • Has its filter_history updated with the split step.

  • Has its $stats slot cleared (preventing stale stats).

  • Passes validate_AlphaVarSet().

Examples

example_file <- system.file("extdata", "bcl11a_rs1427407_example.csv",
                            package = "AlphaVaR")
obj <- av_import_csv(example_file)
#> Reading bcl11a_rs1427407_example.csv ...

by_type <- av_as_subsets(obj, "biosample_type")
names(by_type)
#> [1] "cell_line"                     "in_vitro_differentiated_cells"
#> [3] "organoid"                      "primary_cell"                 
#> [5] "tissue"                       
vapply(by_type, function(x) nrow(x$data), integer(1))
#>                     cell_line in_vitro_differentiated_cells 
#>                           996                           138 
#>                      organoid                  primary_cell 
#>                             8                           632 
#>                        tissue 
#>                           898 

by_type$tissue
#> === AlphaVarSet Object ===
#> Entries:    898 
#> Variants:   2 
#> Modalities: 8 
#> Columns:    25 (incl. 19 extra)
#> Score Mode: quantile_score 
#> Source:     bcl11a_rs1427407_example.csv