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

Installation

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

BiocManager::install("SingleCellMultiModal")

Load packages

library(SingleCellMultiModal)
library(MultiAssayExperiment)

scNMT: single-cell nucleosome, methylation and transcription sequencing

The dataset was graciously provided by @Argelaguet2019-et.

Scripts used to process the raw data were written and maintained by Argelaguet and colleagues and reside on GitHub: https://github.com/rargelaguet/scnmt_gastrulation

For more information on the protocol, see @Clark2018-qg.

Dataset lookup

The user can see the available datasets by using the dry.run argument:

scNMT("mouse_gastrulation", mode = "*", version = "1.0.0", dry.run = TRUE)

Or by simply running the scNMT function with defaults:

scNMT("mouse_gastrulation", version = "1.0.0")

Data versions

A more recent release of the 'mouse_gastrulation' dataset was provided by Argelaguet and colleagues. This dataset includes additional cells that did not pass the original quality metrics as imposed for the version 1.0.0 dataset.

Use the version argument to indicate the newer dataset version (i.e., 2.0.0):

scNMT("mouse_gastrulation", version = '2.0.0', dry.run = TRUE)

Downloading the data

To obtain the data, we can use the mode argument to indicate specific datasets using 'glob' patterns that will match the outputs above. For example, if we would like to have all 'genebody' datasets for all available assays, we would use *_genebody as an input to mode.

nmt <- scNMT("mouse_gastrulation", mode = c("*_DHS", "*_cgi", "*_genebody"),
    version = "1.0.0", dry.run = FALSE)
nmt

Checking the cell metadata

Included in the colData DataFrame within the MultiAssayExperiment class are the variables cellID, stage, lineage10x_2, and stage_lineage. To extract this DataFrame, one has to use colData on the MultiAssayExperiment object:

colData(nmt)

Exploring the data structure

Check row annotations:

rownames(nmt)

The sampleMap is a graph representation of the relationships between cells and 'assay' datasets:

sampleMap(nmt)

Take a look at the cell identifiers or barcodes across assays:

colnames(nmt)

Chromatin Accessibility (acc_*)

See the accessibilty levels (as proportions) for DNase Hypersensitive Sites:

head(assay(nmt, "acc_DHS"))[, 1:4]

DNA Methylation (met_*)

See the methylation percentage / proportion:

head(assay(nmt, "met_DHS"))[, 1:4]

For protocol information, see the references below.

sessionInfo

sessionInfo()

References

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