reduce_taxa {DBTC}

Reduce Taxa Assignment

Description

This function takes a file selection and then uses all '_taxaAssign_YYYY_MM_DD_HHMM.tsv' and/or 'YYYY_MM_DD_HHMM_taxaAssignCombined.tsv' files in that directory and reduces all ASV with the same taxonomic assignment into a single taxonomic result for each submitted file. The results are then placed in to a '_taxaReduced_YYYY_MM_DD_HHMM.tsv' file for each of the target files in the directory.

Usage

reduce_taxa(fileLoc = NULL, numCores = 1, verbose = TRUE)

Arguments

fileLoc

The location of a file in a directory where all of the 'taxaAssign' and/or 'taxaAssignCombine' files are located (Default NULL).

numCores

The number of cores used to run the function (Default 1, Windows systems can only use a single core)

verbose

If set to TRUE then there will be output to the R console, if FALSE then this reporting data is suppressed (Default TRUE).

Details

This function requires a file in a directory where all '_taxaAssign_YYYY_MM_DD_HHMM.tsv' and/or 'YYYY_MM_DD_HHMM_taxaAssignCombined.tsv' files in that directory will be combined. All records with the same taxonomic result will be combined. The BLAST values in parentheses ("Num_Rec", "Coverage", "Identity", "Max_eVal") are combine by the mean number of records, the mean of the minimum coverage and identity values, and the mean of the maximum eValues.

The examples are present to display the syntax for the function. These examples are not run because there are files required to run the functions, in some cases multiple files are necessary and some of these are quite large. To get specific examples please see https://github.com/rgyoung6/DBTCShinyTutorial/blob/main/README.md

Value

This function produces a 'taxa_reduced' file for every 'taxaAssign' or 'taxaAssignCombine' present in the target directory.

Note

WARNING - NO WHITESPACE!

When running DBTC functions the paths for the files selected cannot have white space! File folder locations should be as short as possible (close to the root as some functions do not process long naming conventions.

Also, special characters should be avoided (including question mark, number sign, exclamation mark). It is recommended that dashes be used for separations in naming conventions while retaining underscores for use as information delimiters (this is how DBTC functions use underscore).

There are several key character strings used in the DBTC pipeline, the presence of these strings in file or folder names will cause errors when running DBTC functions.

The following strings are those used in DBTC and should not be used in file or folder naming: - _BLAST - _combinedDada - _taxaAssign - _taxaAssignCombined - _taxaReduced - _CombineTaxaReduced

Author(s)

Robert G. Young

References

<https://github.com/rgyoung6/DBTC> Young, R. G., Hanner, R. H. (Submitted October 2023). Dada-BLAST-Taxon Assign-Condense Shiny Application (DBTCShiny). Biodiversity Data Journal.

See Also

dada_implement() combine_dada_output() make_BLAST_DB() seq_BLAST() taxon_assign() combine_assign_output() combine_reduced_output()

Examples

## Not run: 
reduce_taxa()
reduce_taxa(fileLoc = NULL,   numCores = 1)

## End(Not run)