combine_reduced_output {DBTC}

Combine Reduce Taxa Files for the Same Biological Samples using Different Markers

Description

This function takes a file selection and then uses all 'taxaReduced' files in that directory and combines them into a single taxa table file with presence absence results.The output file is named with the string _CombineTaxaReduced.tsv

Usage

combine_reduced_output(fileLoc = NULL, presenceAbsence = TRUE, verbose = TRUE)

Arguments

fileLoc

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

presenceAbsence

This setting is a TRUE or FASLE value that indicates if the results will include read counts or be reduced to 0/1 presence absence values (Default TRUE)

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

The User Input: This function requires a file in a directory where all 'taxaReduced' files in that directory will be combined. The output format will be a taxa table with all taxa from all files combined into a single table with presence absence (0 or 1) results. The value metrics for the identification of the taxa from each combined file will remain in a column with the parenthetical results from the 'taxaReduced' files ("Num_Rec", "Coverage", "Identity", "Max_eVal").

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 single 'YYYY_MM_DD_HHMM_CombineTaxaReduced' file and associated summary file 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() reduce_taxa()

Examples

## Not run: 
combine_reduced_output()
combine_reduced_output(fileLoc = NULL, presenceAbsence = TRUE)

## End(Not run)