In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleCellMultiModal")

Load libraries

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

CITE-seq dataset

CITE-seq data are a combination of two data types extracted at the same time from the same cell. First data type is scRNA-seq data, while the second one consists of about a hundread of antibody-derived tags (ADT). In particular this dataset is provided by @stoeckius2017simultaneous.

Downloading datasets

The user can see the available dataset by using the default options

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

Or simply by setting dry.run = FALSE it downloads the data and creates the MultiAssayExperiment object.

In this example, we will use one of the two available datasets scADT_Counts:

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

mae

Example with actual data:

experiments(mae)

Exploring the data structure

Check row annotations:

rownames(mae)

Take a peek at the sampleMap:

sampleMap(mae)

scRNA-seq data

The scRNA-seq data are accessible with the name scRNAseq, which returns a matrix object.

head(experiments(mae)$scRNAseq)[, 1:4]

scADT data

The scADT data are accessible with the name scADT, which returns a matrix object.

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

SingleCellExperiment object conversion

Because of already large use of some methodologies (such as in the SingleCellExperiment vignette or CiteFuse Vignette where the SingleCellExperiment object is used for CITE-seq data, we provide a function for the conversion of our CITE-seq MultiAssayExperiment object into a SingleCellExperiment object with scRNA-seq data as counts and scADT data as altExps.

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

Session Info

sessionInfo()

References

waldronlab/SingleCellMultiModal documentation built on May 1, 2024, 5:29 a.m.