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Add Meta-Properties to Experiment

add_meta_properties.Rd

This function adds meta-properties to the variable information of a glyexp::experiment(). Under the hood, it uses get_meta_properties() to calculate the meta-properties on the "glycan_structure" column (or column specified by struc_col) of the variable information tibble, and then adds the result back as new columns.

Usage

add_meta_properties(
  exp,
  mp_fns = NULL,
  struc_col = "glycan_structure",
  overwrite = FALSE
)

Arguments

exp

An glyexp::experiment() object.

mp_fns

A named list of meta-property functions. Names of the list are the names of the meta-properties. Default is all_mp_fns(). A meta-property function should takes a glyrepr::glycan_structure() vector, and returns a vector of the meta-property values. purrr-style lambda functions are supported.

struc_col

The column name of the glycan structures in the variable information tibble. Default is "glycan_structure".

overwrite

Whether to overwrite the existing meta-property columns. Default is FALSE, raising an error if the existing columns are found.

Value

An glyexp::experiment() object with meta-properties added to the variable information.

See also

get_meta_properties(), glyexp::experiment()

Examples

library(glyexp)

# Compare the columns in the variable information before and after adding meta-properties
exp <- real_experiment |>
  slice_sample_var(n = 10)
colnames(get_var_info(exp))
#> [1] "variable"           "peptide"            "peptide_site"      
#> [4] "protein"            "protein_site"       "gene"              
#> [7] "glycan_composition" "glycan_structure"  

exp2 <- add_meta_properties(exp)
colnames(get_var_info(exp2))
#>  [1] "variable"           "peptide"            "peptide_site"      
#>  [4] "protein"            "protein_site"       "gene"              
#>  [7] "glycan_composition" "glycan_structure"   "Tp"                
#> [10] "B"                  "nA"                 "nF"                
#> [13] "nFc"                "nFa"                "nG"                
#> [16] "nGt"                "nS"                 "nM"