Minmax scaling

Perform a minmax standardisation to scale data into 0 to 1 range

minmax(mat)

Arguments

mat

a matrix with rows correspond to phosphosites and columns correspond to condition

Value

Minmax standardised matrix

Examples

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

ppe <- phospho.L6.ratio.pe
sites = paste(sapply(GeneSymbol(ppe), function(x)x),";",
    sapply(Residue(ppe), function(x)x),
    sapply(Site(ppe), function(x)x),
    ";", sep = "")
grps = gsub("_.+", "", colnames(ppe))
design = model.matrix(~ grps - 1)
ctl = which(sites %in% SPSs)
ppe = RUVphospho(ppe, M = design, k = 3, ctl = ctl)

phosphoL6 = SummarizedExperiment::assay(ppe, "normalised")

# filter for up-regulated phosphosites
phosphoL6.mean <- meanAbundance(phosphoL6, grps = grps)
aov <- matANOVA(mat=phosphoL6, grps = grps)
idx <- (aov < 0.05) & (rowSums(phosphoL6.mean > 0.5) > 0)
phosphoL6.reg <- phosphoL6[idx, ,drop = FALSE]

L6.phos.std <- standardise(phosphoL6.reg)

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

data(KinaseMotifs)

numMotif = 5
numSub = 1

motif.mouse.list.filtered <-
    motif.mouse.list[which(motif.mouse.list$NumInputSeq >= numMotif)]
ks.profile.list.filtered <-
    ks.profile.list[which(ks.profile.list$NumSub >= numSub)]

# scoring all phosphosites against all motifs
motifScoreMatrix <-
    matrix(NA, nrow=nrow(L6.phos.std),
    ncol=length(motif.mouse.list.filtered))
rownames(motifScoreMatrix) <- rownames(L6.phos.std)
colnames(motifScoreMatrix) <- names(motif.mouse.list.filtered)

L6.phos.seq <- Sequence(ppe)[idx]

# extracting flanking sequences
seqWin = mapply(function(x) {
    mid <- (nchar(x)+1)/2
    substr(x, start=(mid-7), stop=(mid+7))
}, L6.phos.seq)


print('Scoring phosphosites against kinase motifs:')
#> [1] "Scoring phosphosites against kinase motifs:"
for(i in seq_len(length(motif.mouse.list.filtered))) {
    motifScoreMatrix[,i] <-
        frequencyScoring(seqWin, motif.mouse.list.filtered[[i]])
        cat(paste(i, '.', sep=''))
}
#> 1.2.3.4.5.6.7.8.9.10.11.12.13.14.15.16.17.18.19.20.21.22.23.24.25.26.27.28.29.30.31.32.33.34.35.36.37.38.39.40.41.42.43.44.45.46.47.48.49.50.51.52.53.54.55.56.57.58.59.60.61.62.63.64.65.66.67.68.69.70.71.72.73.74.75.76.77.78.79.80.81.82.83.84.85.86.87.88.89.90.91.92.93.94.95.96.97.98.99.100.101.102.103.104.105.106.107.108.109.110.111.112.113.114.
motifScoreMatrix <- minmax(motifScoreMatrix)