combine_dada_output {DBTC}

Combine Dada Output

Description

This function uses DBTC dada_implement ASV output files (YYYY_MM_DD_HH_MM_UserInputRunName_Merge, YYYY_MM_DD_HH_MM_UserInputRunName_MergeFwdRev, and/or YYYY_MM_DD_HH_MM_UserInputRunName_TotalTable) and combines them into a single ASV table with accompanying fasta file. This function also produces a file containing the processing information for the function. The main input argument for this function is the location of a file in a folder containing all ASV tables wanting to be combined. Output files are generated with the naming convention YYYY_MM_DD_HH_MM_combinedDada.

Usage

combine_dada_output(fileLoc = NULL, minLen = 100, verbose = TRUE)

Arguments

fileLoc

Select a file in the file folder with dada_implement() results you would like to combine (YYYY_MM_DD_HHMM_FileName_MergeFwdRev OR YYYY_MM_DD_HHMM_FileName_Merge both .tsv and .fas files (Default NULL).

minLen

The minimum final desired length of the read (Default 100).

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

Two or more files to be combined are required as input for this function. These files need to be ASV files as outputted from the dada_implement() and can include Merge, MergeFwdRev, or TotalTable.tsv files. In addition, the user can input the desired minimum length of sequences that are wanted in the output combined file.

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

The output from this function includes three files. 1. YYYY_MM_DD_HHMM_combinedDada.tsv - combined ASV table 2. YYYY_MM_DD_HHMM_combinedDada.fas - combined fasta file 3. YYYY_MM_DD_HHMM_combinedDada.txt - Summary file from the combine_dada_output run

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() make_BLAST_DB() seq_BLAST() taxon_assign() combine_assign_output() reduce_taxa() combine_reduced_output()

Examples

## Not run: 
combine_dada_output()
combine_dada_output(fileLoc = NULL, minLen = 100)

## End(Not run)