## ----style, echo = FALSE, results = 'asis', message=FALSE--------------------- BiocStyle::markdown() ## ----setup, message = FALSE, echo = FALSE------------------------------------- library("PSMatch") ## ----------------------------------------------------------------------------- library("PSMatch") id <- msdata::ident(full.names = TRUE, pattern = "TMT") |> PSM() |> filterPsmDecoy() |> filterPsmRank() id ## ----------------------------------------------------------------------------- data.frame(id[1:10, c("sequence", "DatabaseAccess")]) ## ----------------------------------------------------------------------------- adj <- makeAdjacencyMatrix(id) dim(adj) adj[1:5, 1:5] ## ----------------------------------------------------------------------------- length(unique(id$sequence)) length(unique(id$DatabaseAccess)) ## ----------------------------------------------------------------------------- cc <- ConnectedComponents(adj) length(cc) cc ## ----------------------------------------------------------------------------- connectedComponents(cc, 1) ## ----------------------------------------------------------------------------- connectedComponents(cc, 527) ## ----------------------------------------------------------------------------- connectedComponents(cc, 38) ## ----------------------------------------------------------------------------- connectedComponents(cc, 920) ## ----------------------------------------------------------------------------- (i <- which(nrows(cc) > 2 & ncols(cc) > 2)) dims(cc)[i, ] ## ----------------------------------------------------------------------------- cx <- connectedComponents(cc, 1082) cx ## ----------------------------------------------------------------------------- plotAdjacencyMatrix(cx) ## ----------------------------------------------------------------------------- plotAdjacencyMatrix(cx, 1) ## ----------------------------------------------------------------------------- plotAdjacencyMatrix(cx, 2) ## ----------------------------------------------------------------------------- score <- id$MS.GF.RawScore names(score) <- id$sequence head(score) ## ----------------------------------------------------------------------------- cls <- as.character(cut(score, 12, labels = colorRampPalette(c("white", "red"))(12))) names(cls) <- id$sequence head(cls) ## ----------------------------------------------------------------------------- plotAdjacencyMatrix(cx, pepColors = cls) ## ---- message = FALSE--------------------------------------------------------- basename(f <- msdata::quant(full.names = TRUE)) (i <- grep("Intensity\\.", names(read.delim(f)))) library(QFeatures) se <- readSummarizedExperiment(f, ecol = i, sep = "\t") ## ----------------------------------------------------------------------------- prots <- rowData(se)$Proteins names(prots) <- rowData(se)$Sequence head(prots) ## ----------------------------------------------------------------------------- adj <- makeAdjacencyMatrix(prots, split = ";") dim(adj) adj[1:3, 1:3] cc <- ConnectedComponents(adj) cc ## ----------------------------------------------------------------------------- head(cctab <- prioritiseConnectedComponents(cc)) ## ---- message = FALSE--------------------------------------------------------- library(factoextra) fviz_pca(prcomp(cctab, scale = TRUE, center = TRUE)) ## ----si----------------------------------------------------------------------- sessionInfo()