scImpute {PhosR} | R Documentation

## Site- and condition-specific (sc) impute

### Description

Impute the missing values for a phosphosite across replicates within a single condition (or treatment) if there are n or more quantified values of that phosphosite in that condition.

### Usage

    scImpute(mat, percent, grps, assay)

### Arguments

`mat` | a matrix (or PhosphoExperiment object) with rows correspond to phosphosites and columns correspond to replicates within a condition.
`percent` | a percent from 0 to 1, specifying the percentage of quantified values in any treatment group.
`grps` | a string specifying the grouping (replciates).
`assay` | an assay to be selected if `mat` is a PhosphoExperiment object.

### Value

An imputed matrix. If param `mat` is a PhosphoExperiment object, a PhosphoExperiment object will be returned.

### 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)]

    # for PhosphoExperiment Object
    data('phospho.cells.Ins.pe')
    grps = gsub('_[0-9]{1}', '', colnames(phospho.cells.Ins.pe))
    phospho.cells.Ins.filtered <- selectGrps(phospho.cells.Ins.pe, 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)]

[Package PhosR version 1.2.0 Index]