meanAbundance {PhosR} | R Documentation |
Obtain average expression from replicates
meanAbundance(mat, grps)
mat |
a matrix with rows correspond to phosphosites and columns correspond to samples. |
grps |
a string specifying the grouping (replciates). |
a matrix with mean expression from replicates
data('phospho_L6_ratio_pe') data('SPSs') data('PhosphoSitePlus') grps = gsub('_.+', '', colnames(phospho.L6.ratio.pe)) # Construct a design matrix by condition design = model.matrix(~ grps - 1) # phosphoproteomics data normalisation using RUV L6.sites = paste(sapply(GeneSymbol(phospho.L6.ratio.pe), function(x)paste(x)), ";", sapply(Residue(phospho.L6.ratio.pe), function(x)paste(x)), sapply(Site(phospho.L6.ratio.pe), function(x)paste(x)), ";", sep = "") ctl = which(L6.sites %in% SPSs) phospho.L6.ratio.pe = RUVphospho(phospho.L6.ratio.pe, M = design, k = 3,ctl = ctl) phosphoL6 = SummarizedExperiment::assay(phospho.L6.ratio.pe, "normalised") phosphoL6.mean <- meanAbundance(phosphoL6, grps = grps)