scImpute {PhosR} | R Documentation |
Impute the missing values for a phosphosite across replicates within a single condition (or treatment) if there are n or more quantified values of that phosphosite in that condition.
scImpute(mat, percent, grps, assay)
mat |
a matrix (or PhosphoExperiment object) with rows correspond to phosphosites and columns correspond to replicates within a condition. |
percent |
a percent from 0 to 1, specifying the percentage of quantified values in any treatment group. |
grps |
a string specifying the grouping (replciates). |
assay |
an assay to be selected if |
An imputed matrix. If param mat
is a PhosphoExperiment
object, a PhosphoExperiment object will be returned.
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)] # 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 <- scImpute(phospho.cells.Ins.filtered, 0.5, grps)[,colnames(phospho.cells.Ins.filtered)]