siteAnnotate {PhosR} | R Documentation |
This function plots the combined scores of each of all kinases for a given phosphosites
siteAnnotate(site, phosScoringMatrices, predMatrix)
site |
site the ID of a phosphosite |
phosScoringMatrices |
output from function kinaseSubstrateScore() |
predMatrix |
a prediction matrix from kinaseSubstratePred() |
A graphical plot
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) rownames(L6.phos.std) <- paste0(GeneSymbol(ppe), ";", Residue(ppe), Site(ppe), ";")[idx] L6.phos.seq <- Sequence(ppe)[idx] L6.matrices <- kinaseSubstrateScore(PhosphoSite.mouse, L6.phos.std, L6.phos.seq, numMotif = 5, numSub = 1) set.seed(1) L6.predMat <- kinaseSubstratePred(L6.matrices, top=30) dev.off() # We will look at the phosphosite AAK1;S677 for demonstration purpose. site = "AAK1;S677;" siteAnnotate(site, L6.matrices, L6.predMat)