R: Tidy Processing and Analysis of Biological Sequences

# Tidy Processing and Analysis of Biological Sequences

## Documentation for package ‘tidysq’ version 1.2.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

tidysq-package | tidysq: tidy analysis of biological sequences
%has% | Test sq object for presence of given motifs
==.sq | Compare sq objects
alphabet | Get alphabet of given sq object.
as.character.sq | Convert sq object into character vector
as.matrix.sq | Convert sq object into matrix
as.sq | Convert an object to sq
as.sq.character | Convert an object to sq
as.sq.default | Convert an object to sq
bite | Subset sequences from sq objects
bite.sq | Subset sequences from sq objects
collapse | Collapse multiple sequences into one
collapse.sq | Collapse multiple sequences into one
complement | Create complement sequence from dnasq or rnasq object
complement.sq_dna_bsc | Create complement sequence from dnasq or rnasq object
complement.sq_dna_ext | Create complement sequence from dnasq or rnasq object
complement.sq_rna_bsc | Create complement sequence from dnasq or rnasq object
complement.sq_rna_ext | Create complement sequence from dnasq or rnasq object
export_sq | Export sq objects into other formats
find_invalid_letters | Find elements which are not suitable for specified type.
find_invalid_letters.sq | Find elements which are not suitable for specified type.
find_motifs | Find given motifs
find_motifs.data.frame | Find given motifs
find_motifs.sq | Find given motifs
get_sq_lengths | Get lengths of sequences in sq object
get_standard_alphabet | Get standard alphabet for given type.
get_tidysq_options | Obtain current state of tidysq options
import_sq | Import sq objects from other objects
is.sq | Check if object has specified type
is.sq_ami | Check if object has specified type
is.sq_ami_bsc | Check if object has specified type
is.sq_ami_ext | Check if object has specified type
is.sq_atp | Check if object has specified type
is.sq_dna | Check if object has specified type
is.sq_dna_bsc | Check if object has specified type
is.sq_dna_ext | Check if object has specified type
is.sq_rna | Check if object has specified type
is.sq_rna_bsc | Check if object has specified type
is.sq_rna_ext | Check if object has specified type
is.sq_unt | Check if object has specified type
is_empty_sq | Test if sequence is empty
is_empty_sq.sq | Test if sequence is empty
paste | Paste sequences in string-like fashion
paste.sq | Paste sequences in string-like fashion
random_sq | Generate random sequences
read_fasta | Read a FASTA file
remove_ambiguous | Remove sequences that contain ambiguous elements
remove_ambiguous.sq | Remove sequences that contain ambiguous elements
remove_na | Remove sequences that contain NA values
remove_na.sq | Remove sequences that contain NA values
reverse | Reverse sequence
reverse.sq | Reverse sequence
sq | Construct sq object from character vector
sq-class | sq: class for keeping biological sequences tidy
sq-concatenate | Concatenate sq objects
sq-extract | Extract parts of a sq object
sq-print | Print sq object
sqapply | Apply function to each sequence
sqapply.sq | Apply function to each sequence
sqconcatenate | Concatenate sq objects
sqextract | Extract parts of a sq object
sqprint | Print sq object
sq_type | Get type of an sq object
sq_type.sq | Get type of an sq object
sq_type<- | Get type of an sq object
sq_type<-.sq | Get type of an sq object
substitute_letters | Substitute letters in a sequence
substitute_letters.sq | Substitute letters in a sequence
tidysq | tidysq: tidy analysis of biological sequences
tidysq-options | Obtain current state of tidysq options
translate | Convert DNA or RNA into proteins using genetic code
translate.sq_dna_bsc | Convert DNA or RNA into proteins using genetic code
translate.sq_rna_bsc | Convert DNA or RNA into proteins using genetic code
typify | Set type of an sq object
typify.sq | Set type of an sq object
write_fasta | Save sq to fasta file
write_fasta.data.frame | Save sq to fasta file
write_fasta.sq | Save sq to fasta file