medianScaling {PhosR}R Documentation

Median centering and scaling

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)


[Package PhosR version 1.0.0 Index]