make_asv_abund_matrix {demulticoder} | R Documentation |
Make an amplified sequence variant (ASV) abundance matrix for each of the input barcodes
Description
Make an amplified sequence variant (ASV) abundance matrix for each of the input barcodes
Usage
make_asv_abund_matrix(analysis_setup, overwrite_existing = FALSE)
Arguments
analysis_setup |
An object containing directory paths and
data tables, produced by the |
overwrite_existing |
Logical, indicating whether to overwrite existing results. Default is FALSE. |
Details
The function processes data for each unique barcode separately, inferring ASVs, merging reads, and creating an ASV abundance matrix. To do this, the 'DADA2' core denoising alogrithm is used to infer ASVs.
Value
The ASV abundance matrix (asv_abund_matrix
)
Examples
# The primary wrapper function for 'DADA2' ASV inference steps
analysis_setup <- prepare_reads(
data_directory = system.file("extdata", package = "demulticoder"),
output_directory = tempdir(),
overwrite_existing = TRUE
)
cut_trim(
analysis_setup,
cutadapt_path="/usr/bin/cutadapt",
overwrite_existing = TRUE
)
make_asv_abund_matrix(
analysis_setup,
overwrite_existing = TRUE
)
[Package demulticoder version 0.1.2 Index]