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, get.cell=TRUE,
    get.umi=TRUE, get.gem=TRUE, get.gene=TRUE, get.reads=TRUE)

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.

get.cell, get.umi, get.gem, get.gene, get.reads

Logical scalar indicating whether the corresponding field should be extracted.

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.

Setting any of the get.* arguments will (generally) avoid extraction of the corresponding field. This can improve efficiency if that field is not necessary for further analysis. Aside from the missing field, the results are guaranteed to be identical, i.e., same order and number of rows. Note that some fields must be loaded to yield similar results, e.g., gene IDs will always be loaded to remove unmapped reads if keep.unmapped=FALSE.

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 field will not be present in the DataFrame if the corresponding get.* argument is FALSE,

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 1.2.2 Index]