preprocess_alevin: Preprocessing for Alevin output

In rnabioco/scbp: Boilerplate functions for single cell rna-seq analysis

Preprocessing for Alevin output

Description

Preprocessing for Alevin output

Usage

preprocess_alevin(paths, fdr = 0.01, cell_bc = NULL, genes = NULL, ...)

Arguments

paths	paths to salmon output directory with alevin/quants_mat.gz files. If a named vector is supplied then the cellbarcode will be prefixed with "name_".
fdr	fdr cutoff for cell calling
cell_bc	list of character vectors of cell ids to keep in output, if supplied cell calling will be skipped. Order must match paths argument
genes	genes to use for cell calling, useful for exclude mito and ribogenes
...	additional arguments passed onto emptyDrops

Value

A list of named lists with slots: mtx a sparseMatrix with only cell associated barcodes empty_drops a data.frame with information from emptyDrops barcode_ranks a data.frame with information from barcodeRanks

rnabioco/scbp documentation built on July 7, 2023, 10:10 p.m.