matANOVA: ANOVA test

In PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

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')
data('SPSs')

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

# Cleaning phosphosite label
phospho.site.names = rownames(phospho.L6.ratio)
L6.sites = gsub(' ', '', sapply(strsplit(rownames(phospho.L6.ratio), '~'),
                                function(x){paste(toupper(x[2]), x[3], '',
                                                sep=';')}))
phospho.L6.ratio = t(sapply(split(data.frame(phospho.L6.ratio), L6.sites),
                            colMeans))
phospho.site.names = split(phospho.site.names, L6.sites)

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

# phosphoproteomics data normalisation using RUV
ctl = which(rownames(phospho.L6.ratio) %in% SPSs)
phospho.L6.ratio.RUV = RUVphospho(phospho.L6.ratio, M = design, k = 3,
                                ctl = ctl)


phosphoL6 = phospho.L6.ratio.RUV
rownames(phosphoL6) = phospho.site.names

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

PhosR documentation built on Nov. 8, 2020, 6:54 p.m.