## ----quick-start-1, message=FALSE, warning=FALSE------------------------------
library(atacInferCnv)
inPath = system.file("extdata", "MB183_ATAC_subset.tsv.gz", 
                     package = "atacInferCnv")
sAnn = system.file("extdata", "MB183_ATAC_subset.CNV_blocks_ann.txt", 
                   package = "atacInferCnv" )
resPath = tempfile() 

## ----quick-start-3,  message=FALSE, warning=FALSE-----------------------------
prepareAtacInferCnvInput(inPath,sAnn,resPath,
                         targColumn = "cnvBlock",
                          ctrlGrp = "Normal")

## ----quick-start-31,  message=FALSE, warning=FALSE----------------------------
list.files(resPath)

## ----quick-start-4,  message=FALSE, warning=FALSE-----------------------------
iObj <- runAtacInferCnv(resPath,returnObj = TRUE)

## ----quick-start-41,  message=FALSE, warning=FALSE----------------------------
list.files(file.path(resPath,"sample_infercnv"))

## ----quick-start-5,  message=FALSE, warning=FALSE-----------------------------
plots <- plotCnvBlocks(resPath,iObj)
plots[["C1"]]
plots[["C2"]]

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()