## ----eval=FALSE---------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# 
# BiocManager::install("SingleCellMultiModal")

## ----include=TRUE, results="hide", message=FALSE, warning=FALSE---------------

library(MultiAssayExperiment)
library(SingleCellMultiModal)
library(SingleCellExperiment)


## -----------------------------------------------------------------------------

CITEseq(DataType="peripheral_blood", modes="*", dry.run=TRUE, version="1.0.0")


## ----message=FALSE------------------------------------------------------------

mae <- CITEseq(DataType="peripheral_blood", modes="*", dry.run=FALSE, version="1.0.0")
mae

## -----------------------------------------------------------------------------
experiments(mae)

## -----------------------------------------------------------------------------
rownames(mae)

## -----------------------------------------------------------------------------
sampleMap(mae)

## -----------------------------------------------------------------------------
head(experiments(mae)$scRNA)[, 1:4]

## -----------------------------------------------------------------------------
head(experiments(mae)$scADT)[, 1:4]

## -----------------------------------------------------------------------------
(ctclMae <- mae[,colData(mae)$condition == "CTCL",])

## -----------------------------------------------------------------------------
ctclMae[,complete.cases(ctclMae),]

## -----------------------------------------------------------------------------
sgRNAs <- metadata(mae)
names(sgRNAs)

## -----------------------------------------------------------------------------
head(sgRNAs$CTCL_TCRab)

## ----message=FALSE------------------------------------------------------------
sce <- CITEseq(DataType="peripheral_blood", modes="*", dry.run=FALSE, 
               version="1.0.0", DataClass="SingleCellExperiment")
sce

## ----tidy=TRUE----------------------------------------------------------------
sessionInfo()