## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("gscreend") ## ----message=FALSE------------------------------------------------------------ library(gscreend) library(SummarizedExperiment) ## ----------------------------------------------------------------------------- raw_counts <- read.table( system.file("extdata", "simulated_counts.txt", package = "gscreend"), header=TRUE) ## ----------------------------------------------------------------------------- counts_matrix <- cbind(raw_counts$library0, raw_counts$R0_0, raw_counts$R1_0) rowData <- data.frame(sgRNA_id = raw_counts$sgrna_id, gene = raw_counts$Gene) colData <- data.frame(samplename = c("library", "R1", "R2"), # timepoint naming convention: # T0 -> reference, # T1 -> after proliferation timepoint = c("T0", "T1", "T1")) se <- SummarizedExperiment(assays=list(counts=counts_matrix), rowData=rowData, colData=colData) ## ----------------------------------------------------------------------------- pse <- createPoolScreenExp(se) ## ----------------------------------------------------------------------------- pse_an <- RunGscreend(pse) ## ----fig.width=4, fig.height=4.5---------------------------------------------- plotReplicateCorrelation(pse_an) ## ----------------------------------------------------------------------------- plotModelParameters(pse_an) ## ----------------------------------------------------------------------------- res <- ResultsTable(pse_an, direction = "negative") head(res) ## ----------------------------------------------------------------------------- sessionInfo()