kinaseSubstrateScore: Kinase substrate scoring

Description Usage Arguments Value Examples

View source: R/kinaseSubstratePrediction.R

Description

This function generates substrate scores for kinases that pass filtering based on both motifs and dynamic profiles

Usage

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kinaseSubstrateScore(substrate.list, mat, seqs, numMotif = 5, numSub = 1)

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.

seqs

an array containing aa sequences surrounding each of all phosphosites. Each sequence has length of 15 (-7, p, +7).

numMotif

minimum number of sequences used for compiling motif for each kinase. Default is 5.

numSub

minimum number of phosphosites used for compiling phosphorylation profile for each kinase. Default is 1.

Value

A list of 4 elements. motifScoreMatrix, profileScoreMatrix, combinedScoreMatrix, ksActivityMatrix (kinase activity matrix) and their weights.

Examples

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data('phospho_L6_ratio')
data('SPSs')
data('PhosphoSitePlus')

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=';'))})

L6.phos.seq <- sapply(strsplit(rownames(phosphoL6.reg), '~'),
                    function(x)x[4])

L6.matrices <- kinaseSubstrateScore(PhosphoSite.mouse, L6.phos.std,
    L6.phos.seq, numMotif = 5, numSub = 1)

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