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

In ncborcherding/scone: Single-Cell Operation for Neat Enrichment

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

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

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.