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.
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.
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).
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.
Examples
# here we use a dummy fragment file for example:
fragfile <- system.file( "extdata", "example_fragments.tsv.gz",
package="scDblFinder" )
res <- amulet(fragfile)
#> Fragment file is not tabix-indexed, requiring thewhole file to be imported in memory.
#> 08:42:43 - Splitting and subsetting barcodes...
#> 08:42:43 - Obtaining overlaps...