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

This vignette will guide you through how accessing and manipulating the SCoPE2 data sets available from the SingleCellMultimodal package.

Installation

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

Load packages

library(SingleCellMultiModal)
library(MultiAssayExperiment)

SCoPE2

SCoPE2 is a mass spectrometry (MS)-based single-cell proteomics protocol to quantify the proteome of single-cells in an untargeted fashion. It was initially developed by @Specht2021-pm.

Downloading data sets

The user can see the available data set by using the default options.

SCoPE2("macrophage_differentiation",
       mode = "*",
       version = "1.0.0",
       dry.run = TRUE)

Or by simply running:

SCoPE2("macrophage_differentiation")

Available projects

Currently, only the macrophage_differentiation is available.

Retrieving data

You can retrieve the actual data from ExperimentHub by setting dry.run = FALSE. This example retrieves the complete data set (transcriptome and proteome) for the macrophage_differentiation project:

scope2 <- SCoPE2("macrophage_differentiation",
                 modes = "rna|protein",
                 dry.run = FALSE)
scope2

The macrophage differentiation project

This data set has been acquired by the Slavov Lab (@Specht2021-pm). It contains single-cell proteomics and single-cell RNA sequencing data for macrophages and monocytes. The objective of the research that led to generate the data is to understand whether homogeneous monocytes differentiate in the absence of cytokines to macrophages with homogeneous or heterogeneous profiles. The transcriptomic and proteomic acquisitions are conducted on two separate subset of similar cells (same experimental design). The cell type of the samples are known only for the proteomics data. The proteomics data was retrieved from the authors' website and the transcriptomic data was retrieved from the GEO database (accession id: GSE142392).

For more information on the protocol, see @Specht2021-pm.

Data versions

Only version 1.0.0 is currently available.

The macrophage_differentiation data set in this package contains two assays: rna and protein.

Cell annotation

The single-cell proteomics data contains cell type annotation (celltype), sample preparation batch (batch_digest and batch_sort), chromatography batch (batch_chromatography), and the MS acquisition run (batch_MS). The single-cell transcriptomics data was acquired in two batches (batch_Chromium). Note that because the cells that compose the two assays are distinct, there is no common cell annotation available for both proteomics and transcriptomics. The annotation were therefore filled with NAs accordingly.

colData(scope2)

Transcriptomic data

You can extract and check the transcriptomic data through subsetting:

scope2[["rna"]]

The data is rather large and is therefore stored on-disk using the HDF5 backend. You can verify this by looking at the assay data matrix. Note that the counts are UMI counts.

assay(scope2[["rna"]])[1:5, 1:5]

Proteomic data

The protein assay contains MS-based proteomic data. The data have been passed sample and feature quality control, normalized, log transformed, imputed and batch corrected. Detailed information about the data processing is available in another vignette. You can extract the proteomic data similarly to the transcriptomic data:

scope2[["protein"]]

In this case, the protein data have reasonable size and are loaded directly into memory. The data matrix is stored in logexprs. We decided to not use the traditional logcounts because MS proteomics measures intensities rather than counts as opposed to scRNA-Seq.

assay(scope2[["protein"]])[1:5, 1:5]

sessionInfo

sessionInfo()

References

waldronlab/SingleCellMultiModal documentation built on Nov. 3, 2024, 7:32 p.m.