medianScaling: Median centering and scaling

In PengyiYang/PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

Description

Median centering and scaling of an input numeric matrix

Usage

medianScaling(mat, scale = TRUE, grps = NULL, reorder = FALSE)

Arguments

mat	a matrix with rows correspond to phosphosites and columns correspond to samples.
scale	a boolean flag indicating whether to scale the samples.
grps	a string or factor specifying the grouping (replciates).
reorder	whehther to reorder by factor.

Value

A median scaled matrix

Examples

data('phospho.cells.Ins.sample')
grps = gsub('_[0-9]{1}', '', colnames(phospho.cells.Ins))
phospho.cells.Ins.filtered <- selectGrps(phospho.cells.Ins, grps, 0.5, n=1)

set.seed(123)
phospho.cells.Ins.impute <-
    scImpute(phospho.cells.Ins.filtered,
            0.5,
            grps)[,colnames(phospho.cells.Ins.filtered)]

set.seed(123)
phospho.cells.Ins.impute[,1:5] <- ptImpute(phospho.cells.Ins.impute[,6:10],
    phospho.cells.Ins.impute[,1:5], percent1 = 0.6,
    percent2 = 0, paired = FALSE)

phospho.cells.Ins.ms <-
    medianScaling(phospho.cells.Ins.impute, scale = FALSE)

PengyiYang/PhosR documentation built on June 21, 2020, 8:37 a.m.