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, assay = NULL)

### 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` | To reorder the columns by group (`grps`). By default (`reorder=FALSE`), original column order is maintained.
`assay` | an assay to be selected if `mat` is a PhosphoExperiment object.

### 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[,seq(5)] <- ptImpute(
        phospho.cells.Ins.impute[,seq(6,10)],
        phospho.cells.Ins.impute[,seq(5)], percent1 = 0.6,
        percent2 = 0, paired = FALSE)

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

[Package PhosR version 1.2.0 Index]