## ----包括= false ----------------------------------------------------------------------------------------------------------------库（Knitr）opts_chunk $ set（concordance = true）## ---- loadpackage，echo = false，结果='hide' -------------------------------------------------库（ncdfflow）## -----------------------------------------------------------, results='markup'---------------------------- path<-system.file("extdata","compdata","data“，package =“ flowcore”）文件<-list.files（path，fult.names = true）[1：3] nc1 < - read.ncdfflowset（files = files）nc1 ## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------=TRUE, results='hide'--------------------------------------- fs1 <-read.flowset（文件=文件）## ---- unlink，echo = true，结果='markup'------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ nc1 <- read.ncdfFlowSet(files=files, isWriteSlice= FALSE) nc1[[1]] ## ----replacement,echo=TRUE,results='markup'---------------------------------- targetSampleName<-sampleNames(fs1)[1] NC1 [[targetSamplename]] <-fs1 [[1]] NC1 [[1]] NC1 [[2]＃＃＃---- iSempty，echo = true，结果='hide'---------------------------------------------------------------------------------------------------------------------------------------------- NC2 <-clone.ncdfflowset（nc1，isempty = true）nc2 [[1]]] ## ----清理，echo = false，结果='hide'--------------------------------------------------------------------------------------------------------------------------------------------------------- UNINK（NC2）RM（NC2）UNLINK（NC1）RM（NC1）## ----------------------------------------------------------------------------------------------------------------数据（GVHD）GVHD <-GVHD [PDATA（GVHD）$ in％6：7] [1：4] NC1 < -ncdfFlowSet(GvHD) ## ----ncdfFlowSettofs, echo=TRUE,results='markup'------------------------------ fs1<-as.flowSet(nc1,top=2) ## ----metaData, echo=TRUE, results='hide'-------------------------------------- phenoData(nc1) pData(nc1) varLabels(nc1) varMetadata(nc1) sampleNames(nc1) keyword(nc1,"FILENAME") identifier(nc1) colnames(nc1) colnames(nc1,prefix="s6a01") length(nc1) getIndices(nc1,"s6a01") ## ----extraction, echo=TRUE,results='markup'----------------------------------- nm<-sampleNames(nc1)[1] expr1<-paste("nc1$'",nm,"'",sep="") eval(parse(text=expr1)) nc1[[nm]] nm<-sampleNames(nc1)[c(1,3)] nc2<-nc1[nm] summary(nc2) ## ----fsApply, echo=TRUE,results='hide'---------------------------------------- fsApply(nc1,range) fsApply(nc1, each_col, median) ## ----Transformation and compensation, echo=TRUE,results='hide'---------------- cfile <- system.file("extdata","compdata","compmatrix", package="flowCore") comp.mat <- read.table(cfile, header=TRUE, skip=2, check.names = FALSE) comp <- compensation(comp.mat) #compensation summary(nc1)[[1]] nc2<-compensate(nc1, comp) summary(nc2)[[1]] unlink(nc2) rm(nc2) #transformation asinhTrans <- arcsinhTransform(transformationId="ln-transformation", a=1, b=1, c=1) nc2 <- transform(nc1,`FL1-H`=asinhTrans(`FL1-H`)) summary(nc1)[[1]] summary(nc2)[[1]] unlink(nc2) rm(nc2) ## ----Gating, echo=TRUE,results='hide'----------------------------------------- rectGate <- rectangleGate(filterId="nonDebris","FSC-H"=c(200,Inf)) fr <- filter(nc1,rectGate) summary(fr) rg2 <- rectangleGate(filterId="nonDebris","FSC-H"=c(300,Inf)) rg3 <- rectangleGate(filterId="nonDebris","FSC-H"=c(400,Inf)) flist <- list(rectGate, rg2, rg3) names(flist) <- sampleNames(nc1[1:3]) fr3 <- filter(nc1[1:3], flist) summary(fr3[[3]]) ## ----Subsetting, echo=TRUE, results='markup'---------------------------------- nc2 <- Subset(nc1,rectGate) summary(nc2[[1]]) ## ----Subsetting2, echo=FALSE, eval=FALSE-------------------------------------- # nc2 <- Subset(nc1, fr) # summary(nc2[[1]])###this will cause crashing error see #50 # rm(nc2) ## ----Subsetting3, echo=TRUE, results='markup'--------------------------------- library(flowStats) morphGate <- norm2Filter("FSC-H", "SSC-H", filterId = "MorphologyGate",scale = 2) smaller <- Subset(nc1[c(1,3)], morphGate,c("FSC-H", "SSC-H")) smaller[[1]] nc1[[1]] rm(smaller) ## ----split, echo=TRUE--------------------------------------------------------- ##splitting by a gate qGate <- quadGate(filterId="qg", "FSC-H"=200, "SSC-H"=400) fr<-filter(nc1,qGate) ncList<-split(nc1,fr) ncList nc1[[1]] ncList[[2]][[1]] ncList[[1]][[1]] ## ----split2, echo=FALSE, eval=FALSE------------------------------------------- # ncList_new<-split(nc1,fr,isNew=TRUE)###this will cause crashing error see #50