selectTimes: selectTimes

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

selectTimes

Description

selectTimes

Usage

selectTimes(mat, timepoint, order, percent, w, assay)

Arguments

mat	a matrix (or PhosphoExperiment object) with rows correspond to phosphosites and columns correspond to samples in replicates for different treatments.
timepoint	a timepoint as factor with a length equal to the number of columns of mat.
order	a vector specifying the order of timepoints.
percent	a percent (decimal) from 0 to 1, to filter phosphosites with with missing value larger than percent per timepoint.
w	a timepoint window for selection of phosphosites to remove.
assay	an assay to be selected if mat is a PhosphoExperiment object.

Value

a filtered matrix. If param mat is a SummarizedExperiment object, a SummarizedExperiment object will be returned.

Examples

data("phospho_liverInsTC_RUV_sample")
timepoint = gsub("(.*)(\\d+[ms])(.*)", "\\2",
                colnames(phospho.liver.Ins.TC.ratio.RUV))
timepoint[which(timepoint == "0m")] = "0s"
timepoint = factor(timepoint)
timepointOrder = c("0s", "5s", "1m", "2m", "3m", "4m", "6m")

# For demonstration purpose, we introduce missing value at 0s
table(timepoint)

phospho.liver.Ins.TC.sim = phospho.liver.Ins.TC.ratio.RUV
rmId = which(timepoint == "0s")

# We replace the values to NA for the first 26 (~60%) of the '0s' samples
# for the first 100 phosphosite as NA
phospho.liver.Ins.TC.sim[seq(100),rmId[seq(26)]] = NA

phospho.liver.Ins.TC.sim = selectTimes(phospho.liver.Ins.TC.sim,
                                    timepoint, timepointOrder, 0.5,
                                    w = length(table(timepoint)))

# For PhosphoExperiment objects
# mat = PhosR::PhosphoExperiment(
#     assay = phospho.liver.Ins.TC.sim,
#     colData = S4Vectors::DataFrame(
#         timepoint = timepoint
#     )
# )
# phospho.liver.Ins.TC.sim = selectTimes(mat, mat$timepoint, timepointOrder, 
#       0.5, w = length(table(mat$timepoint)))

# Before filtering
dim(phospho.liver.Ins.TC.ratio.RUV)
# After filtering
dim(phospho.liver.Ins.TC.sim)

PYangLab/PhosR documentation built on Nov. 1, 2024, 1:47 p.m.