taxa_counts function

Quantitation of microbes

After identifying true taxa, reads assigned to those taxa are extracted and then undergo a series of filters. The cell barcode and UMI are used to demultiplex the reads and create a barcode x taxa counts matrix. The full taxonomic classification of all resulting barcodes and the number of counts assigned to each clade are tabulated.

taxa_counts(umi_list, samples = NULL)

Arguments

• umi_list: A list of polars DataFrame for UMI data returned by prep_dataset .
• samples: A character of sample identifier for each element in umi_list.

Returns

A polars DataFrame .

Examples

## Not run:

# `umi_list` should be the output of all samples from `prep_dataset()`, and 
# filtered by `slsd()` and `blsd()`
taxa_counts(umi_list, basename(names(umi_list)))
## End(Not run)

See Also

https://github.com/sjdlabgroup/SAHMI