## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----LibraryPreload-------------------------------------------------------- library(TargetSearch) library(TargetSearchData) ## ----cdffiles-------------------------------------------------------------- cdfPath <- tsd_data_path() dir(cdfPath, pattern="cdf$") ## ----samples--------------------------------------------------------------- samples.all <- ImportSamplesFromDir(cdfPath) RIpath(samples.all) <- "." ## ----rim------------------------------------------------------------------- rimLimits <- ImportFameSettings(tsd_file_path("rimLimits.txt")) rimLimits ## ----ricorrect------------------------------------------------------------- RImatrix <- RIcorrect(samples.all, rimLimits, writeCDF4path=FALSE, Window=15, pp.method="ppc", IntThreshold=50) RImatrix ## ----isRIMarker------------------------------------------------------------ isRIMarker <- rep(FALSE, length(samples.all)) isRIMarker[c(1, 6, 11)] <- TRUE ## ----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())