read10xMolInfo {DropletUtils} | R Documentation

## Read the 10X molecule information file

### Description

Extract relevant fields from the molecule information HDF5 file, produced by CellRanger for 10X Genomics data.

### Usage

    read10xMolInfo(sample, barcode.length=NULL, keep.unmapped=FALSE)

### Arguments

`sample` | A string containing the path to the molecule information HDF5 file.
`barcode.length` | An integer scalar specifying the length of the cell barcode.
`keep.unmapped` | A logical scalar indicating whether unmapped molecules should be reported.

### Details

Molecules that were not assigned to any gene have `gene` set to `length(genes)+1`. By default, these are removed when `keep.unmapped=FALSE`.

The length of the cell barcode is automatically inferred if `barcode.length=NULL`. Currently, version 1 of the 10X chemistry uses 14 nt barcodes, while version 2 uses 16 nt barcodes.

### Value

A list is returned containing two elements. The first element is named `data` and is a DataFrame where each row corresponds to a single transcript molecule. The fields are as follows:

`barcode`:

  Character, the cell barcode for each molecule.

`umi`:

  Integer, the processed UMI barcode in 2-bit encoding.

`gem_group`:

  Integer, the GEM group.

`gene`:

  Integer, the index of the gene to which the molecule was assigned. This refers to an entry in the `genes` vector, see below.

`reads`:

  Integer, the number of reads mapped to this molecule.

The second element of the list is named `genes` and is a character vector containing the names of all genes in the annotation. This contains the names of the various entries of `gene` for the individual molecules.

### Author(s)

Aaron Lun, based on code by Jonathan Griffiths

### References

Zheng GX, Terry JM, Belgrader P, and others (2017). Massively parallel digital transcriptional profiling of single cells. Nat Commun 8:14049.

10X Genomics (2017). Molecule info. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/molecule_info

### See Also

`makeCountMatrix`

### Examples

    # Mocking up some 10X HDF5-formatted data.
    out <- DropletUtils:::sim10xMolInfo(tempfile())

    # Reading the resulting file.
    read10xMolInfo(out)

[Package DropletUtils version 1.0.3 Index]