kinaseSubstrateScore {PhosR} | R Documentation

## Kinase substrate scoring

### Description

This function generates substrate scores for kinases that pass filtering based on both motifs and dynamic profiles

### Usage

    kinaseSubstrateScore(
        substrate.list,
        mat,
        seqs,
        numMotif = 5,
        numSub = 1,
        verbose = TRUE
    )

### 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.
`seqs` | an array containing aa sequences surrounding each of all phosphosites. Each sequence has length of 15 (-7, p, +7).
`numMotif` | minimum number of sequences used for compiling motif for each kinase. Default is 5.
`numSub` | minimum number of phosphosites used for compiling phosphorylation profile for each kinase. Default is 1.
`verbose` | Default to `TRUE` to show messages during the progress. All messages will be suppressed if set to `FALSE`

### Value

A list of 4 elements. `motifScoreMatrix`, `profileScoreMatrix`, `combinedScoreMatrix`, `ksActivityMatrix` (kinase activity matrix) and their `weights`.

### 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)

[Package PhosR version 1.2.0 Index]