getSPS {PhosR} | R Documentation |
Generate set of stable phosphoporylated sites
getSPS(phosData, assays, conds, num)
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 |
A vectors of stably phosphorylated sites
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)