## ----style, echo = FALSE, results = 'asis', message=FALSE--------------------- BiocStyle::markdown() ## ----setup, message = FALSE, echo = FALSE------------------------------------- library("PSMatch") ## ----------------------------------------------------------------------------- f <- msdata::ident(full.names = TRUE, pattern = "TMT") basename(f) ## ----------------------------------------------------------------------------- library("PSMatch") id <- PSM(f) id ## ----echo = FALSE------------------------------------------------------------- n_matches <- nrow(id) n_scans <- length(unique(id$spectrumID)) n_seqs <- length(unique(id$sequence)) n_cols <- ncol(id) ## ----------------------------------------------------------------------------- nrow(id) ## number of matches length(unique(id$spectrumID)) ## number of scans length(unique(id$sequence)) ## number of peptide sequences names(id) ## ----------------------------------------------------------------------------- table(id$isDecoy) ## ----------------------------------------------------------------------------- table(table(id$spectrumID)) ## ----------------------------------------------------------------------------- i <- grep("scan=1774", id$spectrumID) id[i, ] id[i, "DatabaseAccess"] ## ----warning = FALSE---------------------------------------------------------- id2 <- reducePSMs(id, id$spectrumID) rownames(id2) <- NULL ## rownames not needed here dim(id2) ## ----------------------------------------------------------------------------- j <- grep("scan=1774", id2$spectrumID) id2[j, ] ## ----------------------------------------------------------------------------- id2[j, "DatabaseAccess"] ## ----------------------------------------------------------------------------- id <- filterPsmDecoy(id) id ## ----------------------------------------------------------------------------- id <- filterPsmRank(id) id ## ----------------------------------------------------------------------------- id[id$sequence == "QKTRCATRAFKANKGRAR", "DatabaseAccess"] ## ----------------------------------------------------------------------------- id <- filterPsmShared(id) id ## ----------------------------------------------------------------------------- id <- PSM(f) filterPSMs(id) ## ----warning = FALSE---------------------------------------------------------- system.time(id1 <- PSM(f, parser = "mzR")) system.time(id2 <- PSM(f, parser = "mzID")) ## ----------------------------------------------------------------------------- names(id1) names(id2) ## ----------------------------------------------------------------------------- nrow(id1) nrow(id2) ## ----------------------------------------------------------------------------- table(id1$isDecoy) table(id2$isdecoy) ## ----------------------------------------------------------------------------- id1_filtered <- filterPSMs(id1) id2_filtered <- filterPSMs(id2) ## ----------------------------------------------------------------------------- identical(sort(unique(id1_filtered$spectrumID)), sort(unique(id2_filtered$spectrumid))) ## ----------------------------------------------------------------------------- anyDuplicated(id2_filtered$spectrumid) ## ----------------------------------------------------------------------------- table(table(id1_filtered$spectrumID)) ## ----------------------------------------------------------------------------- k <- names(which(table(id1_filtered$spectrumID) == 4)) id1_filtered[id1_filtered$spectrumID == k, "sequence"] id1_filtered[id1_filtered$spectrumID == k, "modLocation"] id1_filtered[id1_filtered$spectrumID == k, "modName"] ## ----------------------------------------------------------------------------- id1_filtered$modLocation <- NULL nrow(unique(id1_filtered)) nrow(unique(id2_filtered)) ## ----si----------------------------------------------------------------------- sessionInfo()