tImpute: Tail-based impute

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

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)

PYangLab/PhosR documentation built on Feb. 3, 2024, 3:29 a.m.