Remove Sequences of a DNAbin list object — drop

drop_sequences() removes sequences of a FASTA file by its names.

Usage

drop_sequences(dna, identifier, drop = TRUE)

Arguments

dna: a DNAbin list object.
identifier: a character vector containing sequence names.
drop: Logical. If TRUE, sequence names in identifier will be dropped from dna. If FALSE, sequence names absent in identifier will be dropped instead.

Value

an object of class DNAbin.

Details

drop_sequences() relies on exact match between sequence names within a fasta file and identifier argument.

Author

Pedro S. Bittencourt

Examples


# Create a vector of sequence names to drop or keep.
identifier <- names(geophagus)[1:3]

# Remove sequences listed in identifier
drop_sequences(geophagus, identifier, drop = TRUE)
#> 351 DNA sequences in binary format stored in a list.
#> 
#> All sequences of same length: 690 
#> 
#> Labels:
#> MZ504313.1
#> MZ504311.1
#> MZ504312.1
#> MZ504309.1
#> MZ504341.1
#> MZ504337.1
#> ...
#> 
#> Base composition:
#>     a     c     g     t 
#> 0.237 0.282 0.177 0.303 
#> (Total: 242.19 kb)

# Remove sequences not listed in identifier
drop_sequences(geophagus, identifier, drop = FALSE)
#> 3 DNA sequences in binary format stored in a list.
#> 
#> All sequences of same length: 690 
#> 
#> Labels:
#> MZ504301.1
#> MZ504328.1
#> MZ504318.1
#> 
#> Base composition:
#>     a     c     g     t 
#> 0.237 0.284 0.181 0.298 
#> (Total: 2.07 kb)