medianScaling {PhosR} | R Documentation |
Median centering and scaling of an input numeric matrix
medianScaling(mat, scale = FALSE, grps = NULL, reorder = FALSE, assay = NULL)
mat |
a matrix with rows correspond to phosphosites and columns correspond to samples. |
scale |
a boolean flag indicating whether to scale the samples. |
grps |
a string or factor specifying the grouping (replciates). |
reorder |
To reorder the columns by group ( |
assay |
an assay to be selected if |
A median scaled matrix
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[,seq(5)] <- ptImpute( phospho.cells.Ins.impute[,seq(6,10)], phospho.cells.Ins.impute[,seq(5)], percent1 = 0.6, percent2 = 0, paired = FALSE) phospho.cells.Ins.ms <- medianScaling(phospho.cells.Ins.impute, scale = FALSE)