frequencyScoring {PhosR} | R Documentation

## Frequency scoring

### Description

Frequency scoring

### Usage

    frequencyScoring(sequence.list, frequency.mat)

### Arguments

`sequence.list` | A vector list of sequences
`frequency.mat` | A matrix output from 'createFrequencyMat'

### Value

A vector of frequency score

### Examples

    data('phospho_L6_ratio_pe')
    data('KinaseMotifs')

    # Extracting first 10 sequences for demonstration purpose
    seqs = Sequence(phospho.L6.ratio.pe)
    seqs = seqs[seq(10)]

    # extracting flanking sequences
    seqWin = mapply(function(x) {
        mid <- (nchar(x)+1)/2
        substr(x, start=(mid-7), stop=(mid+7))
    }, seqs)

    # The first 10 for demonstration purpose
    phospho.L6.ratio = SummarizedExperiment::assay(phospho.L6.ratio.pe,
        "Quantification")[seq(10),]

    # minimum number of sequences used for compiling motif for each kinase.
    numMotif=5

    motif.mouse.list.filtered <-
        motif.mouse.list[which(motif.mouse.list$NumInputSeq >= numMotif)]

    # scoring all phosphosites against all motifs
    motifScoreMatrix <-
        matrix(NA, nrow=nrow(phospho.L6.ratio),
            ncol=length(motif.mouse.list.filtered))
    rownames(motifScoreMatrix) <- rownames(phospho.L6.ratio)
    colnames(motifScoreMatrix) <- names(motif.mouse.list.filtered)

    # Scoring phosphosites against kinase motifs
    for(i in seq_len(length(motif.mouse.list.filtered))) {
        motifScoreMatrix[,i] <-
            frequencyScoring(seqWin, motif.mouse.list.filtered[[i]])
        cat(paste(i, '.', sep=''))
    }

[Package PhosR version 1.2.0 Index]