mod.oneway.test: Moderated 1-Way ANOVA

In MKomics: Omics Data Analysis

Description

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

Usage

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

Arguments

x	a (non-empty) numeric matrix of data values.
group	an optional factor representing the groups.
repeated	logical indicating whether there are repeated-measures.
subject	factor with subject IDs; required if repeated = TRUE.
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

Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47.

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

## repeated measures
X <- rbind(matrix(rnorm(6*18), nrow = 6, ncol = 18),
           matrix(rnorm(6*18, mean = 1), nrow = 6, ncol = 18))
gr <- factor(c(rep("T1", 6), rep("T2", 6), rep("T3", 6)))
subjectID <- factor(c(rep(1:6, 3)))
mod.oneway.test(X, gr, repeated = TRUE, subject = subjectID)

MKomics documentation built on Aug. 8, 2021, 5:06 p.m.