Nothing
## ---- 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()
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