frequencyScoring {PhosR} | R Documentation |
Frequency scoring
frequencyScoring(sequence.list, frequency.mat)
sequence.list |
A vector list of sequences |
frequency.mat |
A matrix output from 'createFrequencyMat' |
A vector of frequency score
data('phospho_L6_ratio') data('KinaseMotifs') # Extracting first 10 sequences for demonstration purpose seqs = unlist(lapply(strsplit(rownames(phospho.L6.ratio), "~"), function(i) {i[4]})) seqs = seqs[1:10] # 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 = phospho.L6.ratio[1:10,] # 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='')) }