get10xMolInfoStats: Get 10x cell statistics

In MarioniLab/DropletUtils: Utilities for Handling Single-Cell Droplet Data

Get 10x cell statistics

Description

Compute some basic per-cell statistics from the 10x molecule information file.

Usage

get10xMolInfoStats(sample, barcode.length=NULL, use.library=NULL)

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, see read10xMolInfo.
use.library	An integer vector specifying the library indices for which to extract molecules from sample. Alternatively, a character vector specifying the library type(s), e.g., "Gene expression".

Value

A DataFrame containing one row per cell library, with the fields:

cell:

Character, the cell barcode.

gem_group:

Integer, the GEM group.

num.umis:

Integer, the number of UMIs assigned to this cell barcode/GEM group combination.

num.reads:

Integer, the number of reads for this combination.

num.genes:

Integer, the number of detected genes.

Author(s)

Aaron Lun

See Also

read10xMolInfo

Examples

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

get10xMolInfoStats(out)    

MarioniLab/DropletUtils documentation built on March 14, 2024, 11:04 p.m.