kinaseSubstrateHeatmap {PhosR} | R Documentation

## Kinase-substrate annotation prioritisation heatmap

### Description

Kinase-substrate annotation prioritisation heatmap

### Usage

    kinaseSubstrateHeatmap(phosScoringMatrices, top = 3)

### Arguments

`phosScoringMatrices` | a matrix returned from kinaseSubstrateScore.
`top` | the number of top ranked phosphosites for each kinase to be included in the heatmap. Default is 1.

### Value

a pheatmap object.

### 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)

    kinaseSubstrateHeatmap(L6.matrices)

[Package PhosR version 1.2.0 Index]