get10xMolInfoStats {DropletUtils}R Documentation

Get 10x cell statistics

Description

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

Usage

get10xMolInfoStats(sample, barcode.length=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.

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:::sim10xMolInfo(tempfile())

get10xMolInfoStats(out)    

[Package DropletUtils version 1.2.2 Index]