kinaseSubstrateProfile: Kinase substrate profiling

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

Description

This function generates substrate profiles for kinases that have one or more substrates quantified in the phosphoproteome data.

Usage

kinaseSubstrateProfile(substrate.list, mat)

Arguments

substrate.list	a list of kinases with each element containing an array of substrates.
mat	a matrix with rows correspond to phosphosites and columns correspond to samples.

Value

Kinase profile list.

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)))
phosphoL6.reg <- phosphoL6[(aov < 0.05) &
                        (rowSums(phosphoL6.mean > 0.5) > 0),,drop = FALSE]
L6.phos.std <- standardise(phosphoL6.reg)
rownames(L6.phos.std) <- sapply(strsplit(rownames(L6.phos.std), '~'),
    function(x){gsub(' ', '', paste(toupper(x[2]), x[3], '', sep=';'))})


ks.profile.list <- kinaseSubstrateProfile(PhosphoSite.mouse, L6.phos.std)

PengyiYang/PhosR documentation built on June 21, 2020, 8:37 a.m.