R: MetaboliteANOVA.

MetaboliteANOVA

R Documentation

MetaboliteANOVA.

Description

MetaboliteANOVA will perform an ANOVA on columns of a data matrix according to a specified model.

Usage

MetaboliteANOVA(
  dat = NULL,
  sam = NULL,
  model = NULL,
  method = "none",
  silent = FALSE
)

Arguments

`dat`	Data matrix (e.g. of metabolite).
`sam`	Sample table (same number of row as 'dat' and containing all columns specified in 'model'.
`model`	ANOVA model. May include +, * and : together with column names of sam (cf. Examples).
`method`	The method to be used in column wise multiple testing adjustment, see `p.adjust`.
`silent`	Logical. Shall the function print warnings to the console?

Details

The function is a wrapper for lm including some sanity checks. It will accept a data matrix (traits in columns), sample information (data.frame) and a potential model as input, compute an ANOVA per column and return the respective P-values in a named matrix for further plotting or export.

Value

A named matrix of P-values (rows=metabolites/traits; cols=ANOVA factors).

Examples

# load raw data and sample description
raw <- MetabolomicsBasics::raw
sam <- MetabolomicsBasics::sam
# compute P-values according to specified ANOVA model (simple and complex)
head(m1 <- MetaboliteANOVA(dat = raw, sam = sam, model = "GT"))
head(m2 <- MetaboliteANOVA(dat = raw, sam = sam, model = "GT+Batch+Order+MP"))
# compare P-values for one factor determined in both models
hist(log10(m2[, "GT"]) - log10(m1[, "GT"]), main = "")