getSPS: Generate set of stable phosphoporylated sites

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

Generate set of stable phosphoporylated sites

Description

Generate set of stable phosphoporylated sites

Usage

getSPS(phosData, assays, conds, num)

Arguments

phosData	a list of users' PhosphoExperiment objects from which generate SPSs
assays	an assay to use for each dataset in phosData
conds	a list of vector contains the conditions labels for each sample in the phosphoExperiment objects
num	the number of identified SPSs, by default is 100

Value

A vectors of stably phosphorylated sites

Examples

library(stringr)

data("phospho_L6_ratio_pe")
data("phospho.liver.Ins.TC.ratio.RUV.pe")
data("phospho.cells.Ins.pe")

ppe1 <- phospho.L6.ratio.pe
ppe2 <- phospho.liver.Ins.TC.ratio.RUV.pe
ppe3 <- phospho.cells.Ins.pe
grp3 = gsub('_[0-9]{1}', '', colnames(ppe3))

cond.list <- list(grp1 = gsub("_.+", "", colnames(ppe1)),
                  grp2 = stringr::str_sub(colnames(ppe2), end=-5),
                  grp3 = grp3)

ppe3 <- selectGrps(ppe3, grps = grp3, 0.5, n=1)
ppe3 <- tImpute(ppe3)

# convert matrix to ratio
FL83B.ratio <- SummarizedExperiment::assay(ppe3,"imputed")[, seq(12)] - 
    rowMeans(
        SummarizedExperiment::assay(ppe3,"imputed")[,grep("FL83B_Control", 
        colnames(ppe3))])
Hepa.ratio <- SummarizedExperiment::assay(ppe3,"imputed")[, seq(13,24,1)] - 
    rowMeans(
        SummarizedExperiment::assay(ppe3, "imputed")[,grep("Hepa1.6_Control", 
        colnames(ppe3))])
SummarizedExperiment::assay(ppe3, "Quantification") <- 
    cbind(FL83B.ratio, Hepa.ratio)

ppe.list <- list(ppe1, ppe2, ppe3)

inhouse_SPSs <- getSPS(ppe.list, conds = cond.list)

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