## ----dependencies, warning=FALSE, message=FALSE------------------------------- library(yamss) library(mtbls2) ## ----------------------------------------------------------------------------- filepath <- file.path(find.package("mtbls2"), "mzML") files <- list.files(filepath, pattern = "MSpos-Ex1", recursive = TRUE, full.names = TRUE) classes <- rep(c("wild-type", "mutant"), each = 4) ## ----------------------------------------------------------------------------- colData <- DataFrame(sampClasses = classes, ionmode = "pos") cmsRaw <- readMSdata(files = files, colData = colData, mzsubset = c(500,520), verbose = TRUE) cmsRaw ## ----------------------------------------------------------------------------- cmsProc <- bakedpi(cmsRaw, dbandwidth = c(0.01, 10), dgridstep = c(0.01, 1), outfileDens = NULL, dortalign = TRUE, mzsubset = c(500, 520), verbose = TRUE) cmsProc ## ----------------------------------------------------------------------------- cmsSlice <- slicepi(cmsProc, cutoff = NULL, verbose = TRUE) cmsSlice ## ----------------------------------------------------------------------------- dr <- diffrep(cmsSlice, classes = classes) head(dr) ## ----------------------------------------------------------------------------- topPeaks <- as.numeric(rownames(dr)[1:10]) topPeaks ## ----------------------------------------------------------------------------- bounds <- peakBounds(cmsSlice) idx <- match(topPeaks, bounds[,"peaknum"]) bounds[idx,] ## ----------------------------------------------------------------------------- dmat <- densityEstimate(cmsProc) ## ----------------------------------------------------------------------------- mzrange <- c(bounds[idx[1], "mzmin"], bounds[idx[1], "mzmax"]) scanrange <- c(bounds[idx[1], "scanmin"], bounds[idx[1], "scanmax"]) plotDensityRegion(cmsProc, mzrange = mzrange + c(-0.5,0.5), scanrange = scanrange + c(-30,30)) ## ----------------------------------------------------------------------------- cmsSlice2 <- slicepi(cmsProc, densityCutoff(cmsSlice)*0.99) dqs <- densityQuantiles(cmsProc) head(dqs) cmsSlice3 <- slicepi(cmsProc, dqs["98.5%"]) nrow(peakBounds(cmsSlice)) # Number of peaks detected - original nrow(peakBounds(cmsSlice2)) # Number of peaks detected - updated nrow(peakBounds(cmsSlice3)) # Number of peaks detected - updated ## ----sessionInfo, results='asis', echo=FALSE---------------------------------- sessionInfo()