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Rank metabolites for S2IsoMEr enrichment object

Source: R/MSEA_utils.R
rankScore.Rd

rankScore() ranks metabolites of S2IsoMEr object to perform bootstrapping metabolite set enrichment analysis

Usage

rankScore(object, ranking.by = "wilcox.test", alternative = "greater")

Arguments

object

A S2IsoMEr object.

ranking.by

A character string specifying the ranking method. Options include:

  • "wilcox.test" (default) - Ranks metabolites based on the results of a Wilcoxon test.

  • "t.test" - Ranks metabolites based on the results of a t-test.

  • "logFC" - Ranks metabolites based on log fold change.

  • "BWS" - Ranks metabolites based on BWS (Baumgartner-Weiss-Schindler ).

alternative

A character string specifying the alternative hypothesis for statistical tests. Options are:

  • "two.sided" - Test for differences in both directions.

  • "less" - Test if the second condition is less than the first

  • "greater" - Test if the second condition is greater than the first

Default is "greater".

Value

An object of class S2IsoMEr.

References

Murakami, Hidetoshi. (2012). Modified Baumgartner Statistics for the Two-Sample and Multisample Problems: A Numerical Comparison. Journal of Statistical Computation and Simulation 82 (5): 711–28. https://doi.org/10.1080/00949655.2010.551516

Examples

if (FALSE) { # \dontrun{
data("example_ORA_obj")
example_ORA_obj <-
rankScore(object = example_ORA_obj, ranking.by = 't.test')
} # }