## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----LibraryPreload-------------------------------------------------------- library(TargetSearch) library(TargetSearchData) ## ----cdffiles-------------------------------------------------------------- cdfPath <- file.path(find.package("TargetSearchData"), "gc-ms-data") dir(cdfPath, pattern="cdf$") ## ----samples--------------------------------------------------------------- samples.all <- ImportSamplesFromDir(cdfPath) RIpath(samples.all) <- "." ## ----rim------------------------------------------------------------------- rimLimits <- ImportFameSettings(file.path(cdfPath,"rimLimits.txt")) rimLimits ## ----ricorrect------------------------------------------------------------- RImatrix <- RIcorrect(samples.all, rimLimits, Window=15, pp.method="ppc", IntThreshold=50) RImatrix ## ----isRIMarker------------------------------------------------------------ isRIMarker <- c(T, F, F, F, F, T, F, F, F, F, T, F, F, F, F) ## ----updateRImatrix2------------------------------------------------------- RImatrix2 <- RImatrix RImatrix2[, 2:5] <- RImatrix[,1] RImatrix2[, 7:10] <- RImatrix[,6] RImatrix2[, 12:15] <- RImatrix[,11] ## ----updateRImatrix-------------------------------------------------------- RImatrix2 <- RImatrix z <- cumsum(as.numeric(isRIMarker)) for(i in unique(z)) RImatrix2[, z==i] <- RImatrix[, z==i][,1] RImatrix2 ## ----fixRI----------------------------------------------------------------- fixRI(samples.all, rimLimits, RImatrix2, which(!isRIMarker)) ## ----finally--------------------------------------------------------------- samples <- samples.all[!isRIMarker] RImatrix <- RImatrix2[, !isRIMarker] ## ----sessionInfo, results="asis", echo=FALSE------------------------------- toLatex(sessionInfo())