## ----load_data------------------------------------------------------------- library(synlet) data("exampleDat") head(exampleDat) ## ----zFactor--------------------------------------------------------------- res <- zFactor(exampleDat, negativeCon = "scrambled control si1", positiveCon = "PLK1 si1") head(res) ## ----heatmap--------------------------------------------------------------- plateHeatmap(exampleDat) ## -------------------------------------------------------------------------- scatterPlot(exampleDat, controlOnly = FALSE, colour = rainbow(10), "PLK1 si1", "scrambled control si1", "lipid only") ## ----ZPrime---------------------------------------------------------------- zF_mean <- zFactor(exampleDat, negativeCon = "scrambled control si1", positiveCon = "PLK1 si1") zF_med <- zFactor(exampleDat, negativeCon = "scrambled control si1", positiveCon = "PLK1 si1", useMean = FALSE) ## ----genePlot-------------------------------------------------------------- tem.plot <- siRNAPlot("AAK1", exampleDat, controlsiRNA = c("lipid only", "scrambled control si1"), FILEPATH = ".", zPrimeMed = zF_med, zPrimeMean = zF_mean, treatment = "treatment", control = "control", normMethod = c("PLATE", "lipid only", "scrambled control si1")) ## ----bscore---------------------------------------------------------------- bscore.res <- sapply(as.character(unique(exampleDat$MASTER_PLATE))[1], bScore, exampleDat, control = "control", treatment = "treatment", simplify = FALSE) head(bscore.res$P001) ## ----t_test---------------------------------------------------------------- bscore.ttest <- sapply(names(bscore.res), tTest, bscore.res, numTreat = 3, numCont = 3, simplify = FALSE, USE.NAMES = TRUE) bscore.combined <- data.frame(do.call(rbind, lapply(names(bscore.ttest), function(x) if (!is.null(bscore.ttest[[x]])) {data.frame(MASTER_PLATE = x, siRNAs = rownames(bscore.ttest[[x]]), bscore.ttest[[x]])}))) head(bscore.combined) ## ----madSelection---------------------------------------------------------- madSelection <- sapply(as.character(unique(exampleDat$MASTER_PLATE)), madSelect, exampleDat, control = "control", treatment = "treatment", simplify = FALSE) madSelection.c <- do.call(rbind, lapply(names(madSelection), function(x) madSelection[[x]])) head(madSelection.c) ## ----rankProd-------------------------------------------------------------- rankp.res <- sapply(as.character(unique(exampleDat$MASTER_PLATE)), rankProdHits, exampleDat, control = "control", treatment = "treatment", simplify = FALSE) rankp.c <- data.frame(do.call(rbind, lapply(names(rankp.res), function(x) rankp.res[[x]]))) head(rankp.c) ## ----rsa------------------------------------------------------------------- rsaHits(exampleDat, treatment = "treatment", control = "control", normMethod = "PLATE", LB = 0.2, UB = 0.8, revHits = FALSE, Bonferroni = FALSE, outputFile = "RSAhits.csv") rsa.res <- read.delim("RSAhits.csv", check.names = FALSE) head(rsa.res) ## -------------------------------------------------------------------------- sessionInfo()