scNMT: Single-cell Nucleosome, Methylation and Transcription...

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

Single-cell Nucleosome, Methylation and Transcription sequencing

Description

scNMT assembles data on-the-fly from ExperimentHub to provide a MultiAssayExperiment container. The DataType argument provides access to the mouse_gastrulation dataset as obtained from Argelaguet et al. (2019; DOI: 10.1038/s41586-019-1825-8). Pre-processing code can be seen at https://github.com/rargelaguet/scnmt_gastrulation. Protocol information for this dataset is available at Clark et al. (2018). See the vignette for the full citation.

Usage

scNMT(
  DataType = "mouse_gastrulation",
  modes = "*",
  version = "1.0.0",
  dry.run = TRUE,
  verbose = TRUE,
  ...
)

Arguments

DataType	character(1) Indicates study that produces this type of data (default: 'mouse_gastrulation')
modes	character() A wildcard / glob pattern of modes, such as "acc*". A wildcard of "*" will return all modes including Chromatin Accessibilty ("acc"), Methylation ("met"), RNA-seq ("rna") which is the default.
version	character(1) Either version '1.0.0' or '2.0.0' depending on data version required (default '1.0.0'). See version section.
dry.run	logical(1) Whether to return the dataset names before actual download (default TRUE)
verbose	logical(1) Whether to show the dataset currently being (down)loaded (default TRUE)
...	Additional arguments passed on to the ExperimentHub-class constructor

Details

scNMT is a combination of RNA-seq (transcriptome) and an adaptation of Nucleosome Occupancy and Methylation sequencing (NOMe-seq, the methylome and chromatin accessibility) technologies. For more information, see Reik et al. (2018) DOI: 10.1038/s41467-018-03149-4

• mouse_gastrulation - this dataset provides cell quality control filters in the object colData starting from version 2.0.0. Additionally, cell types annotations are provided through the lineage colData column.

  • rna - RNA-seq

  • acc_\* - chromatin accessibility

  • met_\* - DNA methylation

    • cgi - CpG islands

    • CTCF - footprints of CTCF binding

    • DHS - DNase Hypersensitive Sites

    • genebody - gene bodies

    • p300 - p300 binding sites

    • promoter - gene promoters

Special thanks to Al J Abadi for preparing the published data in time for the 2020 BIRS Workshop, see the link here: https://github.com/BIRSBiointegration/Hackathon/tree/master/scNMT-seq

Value

A single cell multi-modal MultiAssayExperiment or informative data.frame when dry.run is TRUE

versions

Version '1.0.0' of the scNMT mouse_gastrulation dataset includes all of the above mentioned assay technologies with filtering of cells based on quality control metrics. Version '2.0.0' contains all of the cells without the QC filter and does not contain CTCF binding footprints or p300 binding sites.

metadata

The MultiAssayExperiment metadata includes the original function call that saves the function call and the data version requested.

Source

http://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation/

References

Argelaguet et al. (2019)

See Also

SingleCellMultiModal-package

Examples

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

waldronlab/SingleCellMultiModal documentation built on Nov. 23, 2024, 3:46 p.m.