kinaseSubstrateProfile.Rd
This function generates substrate profiles for kinases that have one or more substrates quantified in the phosphoproteome data.
kinaseSubstrateProfile(substrate.list, mat)
Kinase profile list.
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)