siteAnnotate: Phosphosite annotation

In PYangLab/PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

Phosphosite annotation

Description

This function plots the combined scores of each of all kinases for a given phosphosites

Usage

siteAnnotate(site, phosScoringMatrices, predMatrix)

Arguments

site	site the ID of a phosphosite
phosScoringMatrices	output from function kinaseSubstrateScore()
predMatrix	a prediction matrix from kinaseSubstratePred()

Value

A graphical plot

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)

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)

PYangLab/PhosR documentation built on Feb. 3, 2024, 3:29 a.m.