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Calculate mitch enrichment leveraging Rust under the hood

rs_mitch_calc.Rd

[Experimental] Ranks the contrasts column-wise and runs the mitch MANOVA/ANOVA tests per pathway.

Usage

rs_mitch_calc(x, pathway_list, min_size)

Arguments

x

Numerical matrix. Each column represents one of the contrasts you wish to test for and the rows represent the gene statistics per contrast. Needs row names (the genes).

pathway_list

Named list. Each element represents one of the pathways to test for.

min_size

Integer. Minimum size of the gene set to be tested for.

Value

A list with the following elements:

  • pathway_names - The name of the pathway.

  • pathway_sizes - The size of the pathway.

  • manova_pval - The p-value of the MANOVA test.

  • manova_fdr - The Benjamini-Hochberg adjusted manova_pval.

  • anova_pvals - The p-values of the ANOVA test on top of the MANOVA results. Total length = ncol(x) * number of pathways, pathway-major.

  • scores - The scores for each pathway set, contrast. Same length and layout as anova_pvals.

  • s_dist - Calculated distances from the hypotenuse.

  • sd - SDs of the scores.