Showing content from https://www.bioconductor.org/packages/release/bioc/html/../vignettes/flowCut/inst/doc/flowCut.R below:
## ----label=Load_Library, warning=FALSE, message=FALSE, echo=TRUE, fig=FALSE, results='hide'---- library("flowCut") ## ----label=Load_Data, fig=FALSE, results='hide'------------------------------- data(flowCutData) ## ----label=SimpleExample_Image, fig=FALSE, echo=TRUE, height=22, width=22, keep.source=TRUE---- res_flowCut <- flowCut(flowCutData[[1]], FileID = 1, Plot = "All") ## ----label=SimpleExample_Data, fig=FALSE, echo=TRUE--------------------------- res_flowCut$data ## ----label=MaxValleyHgt0p01_Image, fig=FALSE, echo=TRUE, height=22, width=22, keep.source=TRUE---- res_flowCut <- flowCut(flowCutData[[2]], FileID=2, Plot ="All", AllowFlaggedRerun = FALSE, MaxValleyHgt = 0.01) ## ----label=MaxValleyHgt0p1_Image, fig=FALSE, echo=TRUE, height=22, width=22, keep.source=TRUE---- res_flowCut <- flowCut(flowCutData[[2]], FileID=3, Plot ="All", MaxValleyHgt = 0.1) ## ----label=MaxPercCut0p15_Image, fig=FALSE, echo=TRUE, height=22, width=22, keep.source=TRUE---- res_flowCut <- flowCut(flowCutData[[3]], FileID=4, Plot ="All", AllowFlaggedRerun = FALSE, MaxPercCut = 0.15) ## ----label=MaxPercCut0p3_Image, fig=FALSE, echo=TRUE, keep.source=TRUE-------- res_flowCut <- flowCut(flowCutData[[3]], FileID=5, Plot ="All", MaxPercCut = 0.3) ## ----label=EventsRemoved_1---------------------------------------------------- res_flowCut$data["% of events removed",] ## ----label=GateLineForce_44_Image, fig=FALSE, echo=TRUE, height=22, width=22, keep.source=TRUE---- res_flowCut <- flowCut(flowCutData[[3]], FileID=6, Plot ="All", GateLineForce=44) ## ----label=EventsRemoved_2---------------------------------------------------- res_flowCut$data["% of events removed",] ## ----label=AllowFlaggedRerun_UseOnlyWorstChannels_Image_1, fig=FALSE, echo=TRUE, height=22, width=22, keep.source=TRUE---- res_flowCut <- flowCut(flowCutData[[4]], FileID=7, AllowFlaggedRerun = FALSE, Plot ="All") ## ----label=AllowFlaggedRerun_UseOnlyWorstChannels_Image_2, fig=FALSE, echo=TRUE, height=22, width=22, keep.source=TRUE---- res_flowCut <- flowCut(flowCutData[[4]], FileID=8, AllowFlaggedRerun = TRUE, UseOnlyWorstChannels = TRUE, Plot="All")
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