matANOVA {PhosR} | R Documentation

## ANOVA test

### Description

Performs an ANOVA test and returns its adjusted p-value

### Usage

    matANOVA(mat, grps)

### Arguments

`mat` | An p by n matrix where p is the number of phosphosites and n is the number of samples
`grps` | A vector of length n, with group or time point information of the samples

### Value

A vector of multiple testing adjusted p-values

### Examples

    data('phospho_L6_ratio_pe')
    data('SPSs')
    data('PhosphoSitePlus')

    grps = gsub('_.+', '', colnames(phospho.L6.ratio.pe))

    # Construct a design matrix by condition
    design = model.matrix(~ grps - 1)

    # phosphoproteomics data normalisation using RUV
    L6.sites = paste(sapply(GeneSymbol(phospho.L6.ratio.pe), function(x)paste(x)),
                     ";",
                     sapply(Residue(phospho.L6.ratio.pe), function(x)paste(x)),
                     sapply(Site(phospho.L6.ratio.pe), function(x)paste(x)),
                     ";", sep = "")
    ctl = which(L6.sites %in% SPSs)
    phospho.L6.ratio.pe = RUVphospho(phospho.L6.ratio.pe,
                                     M = design, k = 3,ctl = ctl)
    phosphoL6 = SummarizedExperiment::assay(phospho.L6.ratio.pe, "normalised")

    # filter for up-regulated phosphosites
    phosphoL6.mean <- meanAbundance(phosphoL6, grps = grps)
    aov <- matANOVA(mat=phosphoL6, grps = grps)

[Package PhosR version 1.2.0 Index]