taxa_counts: Quantitation of microbes

In rsahmi: Single-Cell Analysis of Host-Microbiome Interactions

Quantitation of microbes

Description

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.

Usage

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.

Value

A polars DataFrame.

See Also

https://github.com/sjdlabgroup/SAHMI

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)

rsahmi documentation built on April 4, 2025, 1:46 a.m.