read10xMolInfo {DropletUtils} | R Documentation |
Extract relevant fields from the molecule information HDF5 file, produced by CellRanger for 10X Genomics data.
read10xMolInfo(sample, barcode.length=NULL, keep.unmapped=FALSE)
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. |
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.
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.
Aaron Lun, based on code by Jonathan Griffiths
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
# Mocking up some 10X HDF5-formatted data. out <- DropletUtils:::sim10xMolInfo(tempfile()) # Reading the resulting file. read10xMolInfo(out)