pmartR (version 2.4.6)

normRes_tests: Test the location and scale parameters from a normalization procedure

Description

Computes p-values from a test of dependence between normalization parameters and group assignment of a normalized omicsData or normRes object

Usage

normRes_tests(norm_obj, test_fn = "kw")

Value

A list with 2 entries containing the p_value of the test performed on the location and scale (if it exists) parameters.

Arguments

norm_obj

object of class 'pepData', 'proData', 'lipidData', 'metabData', 'isobaricpepData', or 'nmrData' that has had normalize_global() run on it, or a 'normRes' object

test_fn

character string indicating the statistical test to use. Current options are "anova" and "kw" for a Kruskal-Wallis test.

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
library(pmartRdata)
mymetab <- edata_transform(omicsData = metab_object, data_scale = "log2")
mymetab <- group_designation(omicsData = mymetab, main_effects = "Phenotype")

# provide the normRes object
mynorm <- normalize_global(omicsData = mymetab, subset_fn = "all",
                           norm_fn = "median", apply_norm = FALSE)
norm_pvals <- normRes_tests(norm_obj = mynorm)

# provide normalized omicsData object
mymetab <- normalize_global(omicsData = mymetab, subset_fn = "all",
                            norm_fn = "median", apply_norm = TRUE)
norm_pvals <- normRes_tests(norm_obj = mymetab)

# NMR data object
mynmr <- edata_transform(omicsData = nmr_identified_object, data_scale = "log2")
mynmr <- group_designation(mynmr, main_effects = "Condition")
mynmrnorm <- normalize_nmr(
  omicsData = mynmr,
  apply_norm = TRUE,
  sample_property_cname = "Concentration"
)
mynmrnorm <- normalize_global(omicsData = mynmrnorm, subset_fn = "all",
                              norm_fn = "median", apply_norm = TRUE, backtransform = TRUE)
norm_pvals <- normRes_tests(norm_obj = mynmrnorm)
}