getSignificance {escape} | R Documentation |
This functions takes the enrichment scores and performs statistical testing to evaluate the difference by group selected. The function can perform 3 tests: 1) linear model based on the limma package, 2) Welch's T test, and 3) one-way ANOVA. The output includes adjusted p-values based on the Benjamini Hochberg method.
getSignificance(enriched, group = NULL, fit = "linear.model")
enriched |
The output of |
group |
The parameter to group for the comparison, should a column of the enriched input |
fit |
The test used for significance, either linear.model, ANOVA, or T.test |
Data frame of test statistics
enrichIt
for generating enrichment scores.
ES2 <- readRDS(url( "https://ncborcherding.github.io/vignettes/escape_enrichment_results.rds")) output <- getSignificance(ES2, group = "Type", fit = "linear.model")