amulet: amulet

In plger/scDblFinder: scDblFinder

amulet

Description

ATACseq (Thibodeau, Eroglu, et al., Genome Biology 2021). The rationale is that cells with unexpectedly many loci covered by more than two reads are more likely to be doublets.

Usage

amulet(x, ...)

Arguments

x	The path to a fragments file, or a GRanges object containing the fragments (with the 'name' column containing the barcode, and the 'score' column containing the count).
...	Any argument to getFragmentOverlaps.

Details

When used on normal (or compressed) fragment files, this implementation is relatively fast (except for reading in the data) but it has a large memory footprint since the overlaps are performed in memory. It is therefore recommended to compress the fragment files using bgzip and index them with Tabix; in this case each chromosome will be read and processed separately, leading to a considerably lower memory footprint. See the underlying getFragmentOverlaps for details.

Value

A data.frame including, for each barcode, the number sites covered by more than two reads, the number of reads, and p- and q-values (low values indicative of doublets).

Examples

# here we use a dummy fragment file for example:
fragfile <- system.file( "extdata", "example_fragments.tsv.gz",
                         package="scDblFinder" )
res <- amulet(fragfile)

plger/scDblFinder documentation built on March 20, 2024, 9:46 p.m.