kinaseSubstrateProfile {PhosR} | R Documentation |
This function generates substrate profiles for kinases that have one or more substrates quantified in the phosphoproteome data.
kinaseSubstrateProfile(substrate.list, mat)
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. |
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)