selectOverallPercent: Select phosphosite by percentage of quantification

Description Usage Arguments Value Examples

View source: R/filter.R

Description

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

Usage

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selectOverallPercent(mat, percent=NULL, n=NULL)

Arguments

mat

a matrix 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.

Value

a filtered matrix

Examples

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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)

PengyiYang/PhosR documentation built on June 21, 2020, 8:37 a.m.