getSignificance: Perform significance testing between groups and enrichement...

Description Usage Arguments Value See Also Examples

View source: R/significance.R

Description

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. The input

Usage

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getSignificance(enriched, group = NULL, fit = "linear.model")

Arguments

enriched

The output of enrichIt.

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

Value

Data frame of test statistics

See Also

EnrichIt for generating enrichment scores.

Examples

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ES2 <- readRDS(url(
"https://ncborcherding.github.io/vignettes/scone_enrichment_results.rds"))
output <- GetSignificance <- function(enriched, group = "Type",
output <- getSignificance(ES2, group = "Type",
fit = "linear.model")

ncborcherding/scone documentation built on Sept. 5, 2020, 1:11 a.m.