selectGrps {PhosR} | R Documentation

## Select by treatment groups (replicate block)

### Description

Select phosphosites that have been quantified in a given percentage of treatment groups (e.g. 0.75 as 3 out of 4 replicates) in n groups.

### Usage

    selectGrps(mat, grps, percent, n, assay)

### Arguments

`mat` | a matrix (PhosphoExperiment object) with rows correspond to phosphosites and columns correspond to samples in replicates for different treatments.
`grps` | a string specifying the grouping (replicates).
`percent` | a percent from 0 to 1, specifying the percentage of quantified values in any treatment group.
`n` | an integer indicating n or more replicates pass the percentage filtering for a phosphosite to be included.
`assay` | an assay to be selected if `mat` is a PhosphoExperiment object.

### Value

a filtered matrix (or a PhosphoExperiment Oject) with at least 'percent' quantification in one or more conditions. If an input `mat` is a SummarizedExperiment object, filtered SummarizedExperiment object will be returned.

### Author(s)

Pengyi Yang, Taiyun Kim

### 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)

    # 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)

[Package PhosR version 1.2.0 Index]