getSPS {PhosR} | R Documentation

## 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)

[Package PhosR version 1.2.0 Index]