mod.oneway.test: Moderated 1-Way ANOVA

In stamats/MKmisc: Miscellaneous Functions from M. Kohl

Moderated 1-Way ANOVA

Description

Performs moderated 1-Way ANOVAs based on Bioconductor package limma.

Usage

mod.oneway.test(x, group, adjust.method = "BH", sort.by = "none")

Arguments

x	a (non-empty) numeric matrix of data values.
group	an optional factor representing the groups.
adjust.method	see p.adjust
sort.by	see toptable

, where "logFC" corresponds to difference in means.

Details

The function uses Bioconductor package limma to compute moderated 1-way ANOVAs. For more details we refer to ebayes.

Value

A data.frame with the results.

References

B. Phipson, S. Lee, I.J. Majewski, W.S. Alexander, G.H. Smyth (2016). Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. Annals of Applied Statistics 10(2), 946-963.

See Also

oneway.test, mod.t.test

Examples

set.seed(123)
X <- rbind(matrix(rnorm(5*20), nrow = 5, ncol = 20),
           matrix(rnorm(5*20, mean = 1), nrow = 5, ncol = 20))
gr <- factor(c(rep("A1", 5), rep("B2", 5), rep("C3", 5), rep("D4", 5)))
mod.oneway.test(X, gr)

## Welch 1-Way ANOVA (not moderated)
ow.test <- function(x, g){
  res <- oneway.test(x ~ g)
  c(res$statistic, res$p.value)
}
ow.res <- t(apply(X, 1, ow.test, g = gr))
colnames(ow.res) <- c("F", "p.value")
ow.res

stamats/MKmisc documentation built on Nov. 20, 2022, 6:06 a.m.