tImpute {PhosR} | R Documentation

## Tail-based impute

### Description

Tail-based imputation approach as implemented in Perseus.

### Usage

    tImpute(mat, m, s, assay)

### Arguments

`mat` | a matrix (or PhosphoExperiment object) with rows correspond to phosphosites and columns correspond to samples.
`m` | a numeric number for controlling mean downshifting.
`s` | a numeric number for controlling standard deviation of downshifted sampling values.
`assay` | an assay to be selected if `mat` is a PhosphoExperiment object.

### Value

An imputed matrix. If param `mat` is a SummarizedExperiment object, a SummarizedExperiment 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 <- tImpute(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 <- tImpute(phospho.cells.Ins.filtered)

[Package PhosR version 1.2.0 Index]