Tail-based impute — tImpute • PhosR

Tail-based imputation approach as implemented in Perseus.

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)