get_spans_params {pmartR}

Gets the parameters for the highest ranked methods from spans.

Description

Gets the parameters for the highest ranked methods from spans.

Usage

get_spans_params(SPANSRes_obj, sort_by_nmols = FALSE)

Arguments

SPANSRes_obj

an object of the class SPANSRes obtained by calling spans_procedure()

sort_by_nmols

a logical indicator of whether to sort by number of molecules used in the normalization (see spans_procedure for info about the 'mols_used_in_norm' column)

Value

A list of lists, where there are multiple sublists only if there were ties for the top SPANS score. Each sublist contains named elements for the subset and normalization methods, and the parameters used for the subset method.

Examples

library(pmartRdata)

# data must be log transformed and grouped
myobject <- edata_transform(omicsData = pep_object, data_scale = "log2")
myobject <- group_designation(omicsData = myobject, main_effects = "Phenotype")

spans_result <- spans_procedure(omicsData = myobject)

# a list of the parameters for any normalization procedure with the best SPANS score
best_params <- get_spans_params(spans_result)

# extract the arguments from the first list element
subset_fn = best_params[[1]]$subset_fn
norm_fn = best_params[[1]]$norm_fn
params = best_params[[1]]$params
if (is.null(params[[1]])) {
  params = NULL
}

# pass arguments to normalize global
norm_object <- normalize_global(omicsData = myobject, subset_fn = subset_fn,
                                norm_fn = norm_fn, params = params)