ReadAlevin: Load alevin quantification data

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Load alevin quantification data

Description

A wrapper around tximport to create a SeuratObject from alevin quantification data.

Usage

ReadAlevin(file, getMeta = FALSE, meanAndVariance = FALSE, ...)

Arguments

file	path to quants_mat.gz file within alevin directory
getMeta	logical, option to use tximeta to programmatically obtain gene range information, default is FALSE. Ranges are stored in chr, start, and end in the meta.features slot.
meanAndVariance	logical, should mean and variance of counts be returned in counts and data slots, respectively
...	extra arguments passed to tximport, for example, alevinArgs=list(filterBarcodes=TRUE).

Value

returns a Seurat object with alevin counts

Author(s)

Avi Srivastava

References

Srivastava, Avi, et al. "Alevin efficiently estimates accurate gene abundances from dscRNA-seq data." Genome biology 20.1 (2019): 65.

See Also

alevin

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.