selectOverallPercent {PhosR} | R Documentation

## Select phosphosite by percentage of quantification

### Description

Select phosphosites that have been quantified in more than a given percentage of samples

### Usage

    selectOverallPercent(mat, percent, n, assay)

### Arguments

`mat` | a matrix (or PhosphoExperiment object) with rows correspond to phosphosites and columns correspond to samples in replicates for different treatments.
`percent` | a percent from 0 to 1, specifying the percentage of quantified values in across all samples for retaining a phosphosite for subsequent analysis.
`n` | an integer indicating n or more quantified values required for retaining a phosphosite for subsequent analysis.
`assay` | an assay to be selected if `mat` is a PhosphoExperiment object.

### Value

a filtered matrix

### Examples

    data('phospho.cells.Ins.sample')

    phospho.cells.Ins.filtered <- selectOverallPercent(phospho.cells.Ins, 0.5)

    # Before filtering
    dim(phospho.cells.Ins)
    # After filtering
    dim(phospho.cells.Ins.filtered)

[Package PhosR version 1.2.0 Index]