selectOverallPercent: Select phosphosite by percentage of quantification

In PYangLab/PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

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)

PYangLab/PhosR documentation built on Nov. 1, 2024, 1:47 p.m.