ptImpute: Paired-tail (pt) based impute

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

Description

Impute the missing values for mat2 using tail imputation approach if mat1 has more than percent1 (percentage) of quantified values and mat2 has less than percent2 (percentage) quantified values, and vice versa if paired is set to be true. That is if mat2 has percentage of quantified values more than percent1 and mat1 has percentage quantified values less than percent2.

Usage

ptImpute(mat1, mat2, percent1, percent2, m, s, paired)

Arguments

mat1	a matrix with rows correspond to phosphosites and columns correspond to replicates within treatment1.
mat2	a matrix with rows correspond to phosphosites and columns correspond to replicates within treatment2.
percent1	a percent indicating minimum quantified percentages required for considering for imputation.
percent2	a percent indicating minimum quantified percentages required for considering for imputation.
m	a numeric number of for controlling mean downshifting.
s	a numeric number of for controlling standard deviation of downshifted sampling values.
paired	a flag indicating whether to impute for both treatment1 and treatment2 (default) or treatment2 only (if paired=FALSE).

Value

An imputed matrix

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 <-
    scImpute(
    phospho.cells.Ins.filtered,
    0.5,
    grps)[,colnames(phospho.cells.Ins.filtered)]

set.seed(123)
phospho.cells.Ins.impute[,1:5] <- ptImpute(phospho.cells.Ins.impute[,6:10],
phospho.cells.Ins.impute[,1:5], percent1 = 0.6, percent2 = 0, paired = FALSE)

PhosR documentation built on Nov. 8, 2020, 6:54 p.m.