kinaseSubstrateProfile {PhosR} | R Documentation

## Kinase substrate profiling

### Description

This function generates substrate profiles for kinases that have one or more substrates quantified in the phosphoproteome data.

### Usage

    kinaseSubstrateProfile(substrate.list, mat)

### Arguments

`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.

### Value

Kinase profile list.

### 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)

[Package PhosR version 1.2.0 Index]