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Checks for Differences Between Identifiers in Metadata and DNA Sequence Files

Source: R/check_identifiers.R
check_identifiers.Rd

check_identifiers() checks for differences between identifiers in metadata and DNA sequence files.

Usage

check_identifiers(dna, identifier, data)

Arguments

dna

a DNAbin object.

identifier

column in data which contains sequence identifiers.

data

an object of class tbl_df containing sequence metadata.

Value

Invisibly returns TRUE if all checks pass.

Details

check_identifiers() is a helper function to check for inconsistencies between identifiers in metadata and DNA sequence files. It performs three checks, in order:

  1. every identifier in dna must be present in data; any missing identifiers are reported and abort the function.

  2. dna must not contain duplicated identifiers; any duplicates are reported and abort the function.

  3. data must not contain duplicated identifiers. Duplicated identifiers that also occur in dna are reported and abort the function, since they make matching sequences to metadata ambiguous. Duplicated identifiers that do not occur in dna are reported as a warning only, since they do not affect matching.

Author

Pedro S. Bittencourt, Rupert A. Collins.

Examples

check_identifiers(geophagus, "gbAccession", geophagus_info)
#> ✔ Identifiers passed all checks.