Help for package bioseq

Type:

Package

Title:

A Toolbox for Manipulating Biological Sequences

Version:

0.1.4

Maintainer:

Francois Keck <francois.keck@gmail.com>

Description:

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.

License:

GPL-3

URL:

https://fkeck.github.io/bioseq/

BugReports:

https://github.com/fkeck/bioseq/issues

Encoding:

UTF-8

LazyData:

true

Depends:

R (≥ 3.1.0)

Imports:

methods, vctrs, tibble, ape, crayon, dplyr, pillar, stringi, stringr, stringdist, readr, rlang

Suggests:

knitr, rmarkdown, testthat (≥ 2.1.0), covr

VignetteBuilder:

knitr

RoxygenNote:

7.2.1

NeedsCompilation:

Packaged:

2022-08-12 12:49:49 UTC; ecoadmin

Author:

Francois Keck

[aut, cre, cph]

Repository:

CRAN

Date/Publication:

2022-09-06 11:40:18 UTC

bioseq: A Toolbox for Manipulating Biological Sequences

Description

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) doi: 10.1111/2041-210X.13490. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.

Author(s)

Maintainer: Francois Keck francois.keck@gmail.com (ORCID) [copyright holder]

Build an amino acid (AA) vector

Description

aa() build a AA vector from a character vector.

Usage

aa(...)

Arguments

...

character to turn into AA. Can be a set of name-value pairs.

Value

vector of class bioseq_aa

Examples


aa("AGGTGC", "TTCGA")

aa(Seq_1 = "AGGTGC", Seq_2 = "TTCGA")

x <- c("AGGTGC", "TTCGA")
aa(x)

AliView: DNA sequences viewer

Description

This function uses AliView (Larsson, 2014) to visualize DNA sequences. The software must be installed on the computer.

Usage

aliview(
  x,
  aliview_exec = getOption("bioseq.aliview.exec", default = "aliview")
)

Arguments

x

a DNA, RNA or AA vector. Alternatively a DNAbin or AAbin object.

aliview_exec

a character string giving the path of the program.

Details

By default, the function assumes that the executable is installed in a directory located on the PATH. Alternatively the user can provide an absolute path to the executable (i.e. the location where the software was installed/uncompressed). This information can be stored in the global options settings using options(bioseq.aliview.exec = "my_path_to_aliview").

References

Larsson, A. (2014). AliView: a fast and lightweight alignment viewer and editor for large data sets. Bioinformatics 30(22): 3276-3278.

Biological alphabets

Description

List of the allowed characters for each type of sequences.

DNA

A C G T W S M K R Y B D H V N -

RNA

A C G U W S M K R Y B D H V N -

AA

A C D E F G H I K L M N P Q R S T V W Y B X Z J U O * -

References

Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1986). Proc. Natl. Acad. Sci. USA. 83 (1): 4–8.

Nomenclature and Symbolism for Amino Acids and Peptides. IUPAC-IUB Joint Commission on Biochemical Nomenclature. 1983.

Convert DNAbin/AAbin to tibble

Description

These methods convert sequences from ape formats DNAbin and AAbin to tibbles.

Usage

as_tibble.DNAbin(x, label = "label", sequence = "sequence", ...)

as_tibble.AAbin(x, label = "label", sequence = "sequence", ...)

Arguments

x

a DNAbin or AAbin object.

label

Name of the column that stores the sequence labels in the returned tibble.

sequence

Name of the column that stores the sequences in the returned tibble.

...

Not used.

Value

A tibble with two columns (if name is not NULL, the default) or one column (otherwise).

Examples

require(ape)
require(tibble)
x <- rDNAbin(nrow = 10, ncol = 25)
as_tibble.DNAbin(x)

Convert bioseq DNA, RNA and AA to tibble

Description

Convert bioseq DNA, RNA and AA to tibble

Usage

as_tibble.bioseq_dna(x, label = "label", sequence = "sequence", ...)

as_tibble.bioseq_rna(x, label = "label", sequence = "sequence", ...)

as_tibble.bioseq_aa(x, label = "label", sequence = "sequence", ...)

Arguments

x

a DNA, RNA or AA vector.

label

Name of the column that stores the sequence labels in the returned tibble.

sequence

Name of the column that stores the sequences in the returned tibble.

...

Not used.

Value

A tibble with two columns (if name is not NULL, the default) or one column (otherwise).

Examples


require(tibble)
x <- dna(A = "ACGTTAGTGTAGCCGT", B = "CTCGAAATGA", C = NA)
as_tibble(x)

Coerce to AAbin

Description

Coerce to AAbin

Usage

as_AAbin(x, ...)

Arguments

x

An object.

...

Other parameters.

Value

An AAbin object.

Coerce tibble to AAbin

Description

Coerce tibble to AAbin

Usage

## S3 method for class 'tbl_df'
as_AAbin(x, sequences, labels = NULL, ...)

Arguments

x

a tibble.

sequences

Name of the tibble column that stores the sequences.

labels

Name of the tibble column that stores the sequence labels.

...

Other params.

Value

An AAbin object.

Coerce to DNAbin

Description

Coerce to DNAbin

Usage

as_DNAbin(x, ...)

Arguments

x

An object.

...

Other parameters.

Value

A DNAbin object.

Coerce tibble to DNAbin

Description

Coerce tibble to DNAbin

Usage

## S3 method for class 'tbl_df'
as_DNAbin(x, sequences, labels = NULL, ...)

Arguments

x

a tibble.

sequences

Name of the tibble column that stores the sequences.

labels

Name of the tibble column that stores the sequence labels.

...

Other params.

Value

A DNAbin object.

Coercion to an amino acid (AA) vector

Description

Coercion to an amino acid (AA) vector

Usage

as_aa(x)

Arguments

x

An object to coerce.

Value

An amino acid vector of class bioseq_aa

Coercion to DNA vector

Description

Coercion to DNA vector

Usage

as_dna(x)

Arguments

x

An object to coerce.

Value

A DNA vector of class bioseq_dna

Coercion to RNA vector

Description

Coercion to RNA vector

Usage

as_rna(x)

Arguments

x

An object to coerce.

Value

A RNA vector of class bioseq_rna

Coerce to seqinr alignment

Description

Coerce to seqinr alignment

Usage

as_seqinr_alignment(x, ...)

Arguments

x

An object.

...

Other parameters.

Value

An alignment object.

Genetic code tables

Description

The function returns a list of named vectors with Start, Stop and Full_name attributes.

Usage

dic_genetic_codes()

Value

A list of genetic code tables for DNA/RNA translation.

Build a DNA vector

Description

dna() build a DNA vector from a character vector.

Usage

dna(...)

Arguments

...

characters to turn into DNA. Can be a set of name-value pairs.

Value

a vector of class bioseq_dna

Examples


dna("AGGTGC", "TTCGA")

dna(Seq_1 = "AGGTGC", Seq_2 = "TTCGA")

x <- c("AGGTGC", "TTCGA")
dna(x)

DNA sequences (rbcL) for various Fragilaria

Description

An unparsed FASTA of DNA sequences (rbcL) for various strains of Fragilaria retrieved from NCBI.

Usage

fragilaria

Format

A long character vector (unparsed FASTA).

Source

GenBank https://www.ncbi.nlm.nih.gov/genbank/ using the following search term: "(rbcl) AND Fragilaria"

Genetic code tables

Description

List of all genetic code tables available in bioseq. The number in bold can be used to select a table in appropriate functions.

Available genetic codes

1. Standard

2. Vertebrate Mitochondrial

3. Yeast Mitochondrial

4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma

5. Invertebrate Mitochondrial

6. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear

9. Echinoderm Mitochondrial; Flatworm Mitochondrial

10. Euplotid Nuclear

11. Bacterial, Archaeal and Plant Plastid

12. Alternative Yeast Nuclear

13. Ascidian Mitochondrial

14. Alternative Flatworm Mitochondrial

15. Blepharisma Macronuclear

16. Chlorophycean Mitochondrial

21. Trematode Mitochondrial

22. Scenedesmus obliquus Mitochondrial

23. Thraustochytrium Mitochondrial

24. Pterobranchia Mitochondrial

25. Candidate Division SR1 and Gracilibacteria

26. Pachysolen tannophilus Nuclear

27. Karyorelict Nuclear

28. Condylostoma Nuclear

29. Mesodinium Nuclear

30. Peritrich Nuclear

31. Blastocrithidia Nuclear

32. Balanophoraceae Plastid

33. Cephalodiscidae Mitochondrial

References

Andrzej (Anjay) Elzanowski and Jim Ostell at National Center for Biotechnology Information (NCBI), Bethesda, Maryland, U.S.A. https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes

Test if the object is an amino acid vector

Description

This function returns TRUE for objects of class bioseq_aa

Usage

is_aa(x)

Arguments

x

An object.

Value

Logical.

Examples

x <- c("AGGTGC", "TTCGA")
is_aa(x)
y <- aa(x)
is_aa(x)

Test if the object is a DNA vector

Description

This function returns TRUE for objects of class bioseq_dna

Usage

is_dna(x)

Arguments

x

An object.

Value

Logical.

Examples

x <- c("AGGTGC", "TTCGA")
is_dna(x)
y <- dna(x)
is_dna(y)

Test if the object is a RNA vector

Description

This function returns TRUE for objects of class bioseq_rna

Usage

is_rna(x)

Arguments

x

An object.

Value

Logical.

Examples

x <- c("AGGTGC", "TTCGA")
is_rna(x)
y <- rna(x)
is_rna(x)

Amino acid (AA) vector constructor

Description

Amino acid (AA) vector constructor

Usage

new_aa(x = character())

Arguments

x

a character vector.

DNA vector constructor

Description

DNA vector constructor

Usage

new_dna(x = character())

Arguments

x

a character vector.

RNA vector constructor

Description

RNA vector constructor

Usage

new_rna(x = character())

Arguments

x

a character vector.

Internal formatting

Description

Internal formatting

Usage

pillar_shaft.bioseq_aa(x, ...)

Arguments

x

a object.

...

other params.

Internal formatting

Description

Internal formatting

Usage

pillar_shaft.bioseq_dna(x, ...)

Arguments

x

an object.

...

other params.

Internal formatting

Description

Internal formatting

Usage

pillar_shaft.bioseq_rna(x, ...)

Arguments

x

a object.

...

other params.

Read sequences in FASTA format

Description

Read sequences in FASTA format

Usage

read_fasta(file, type = "DNA")

Arguments

file

A path to a file, a connection or a character string.

type

Type of data. Can be "DNA" (the default), "RNA" or "AA".

Value

A DNA, RNA or AA vector (depending on type argument).

Reverse and complement sequences

Description

Reverse and complement sequences

Usage

seq_complement(x)

seq_reverse(x)

Arguments

x

a DNA or RNA vector. Function seq_reverse also accepts AA vectors.

Value

A reverse or complement sequence (same class as the input).

Examples

x <- dna("ACTTTGGCTAAG")
seq_reverse(x)
seq_complement(x)

Build a RNA vector

Description

rna() build a RNA vector from a character vector.

Usage

rna(...)

Arguments

...

characters to turn into RNA. Can be a set of name-value pairs.

Value

a vector of class bioseq_rna

Examples


rna("AGGUGC", "UUCGA")

rna(Seq_1 = "AGGUGC", Seq_2 = "UUCGA")

x <- c("AGGTGC", "TTCGA")
rna(x)

SeaView: DNA sequences and phylogenetic tree viewer

Description

This function opens SeaView (Gouy, Guindon & Gascuel, 2010) to visualize biological sequences and phylogenetic trees. The software must be installed on the computer.

Usage

seaview(
  x,
  seaview_exec = getOption("bioseq.seaview.exec", default = "seawiew")
)

Arguments

x

a DNA, RNA or AA vector. Alternatively a DNAbin or AAbin object or a phylogenetic tree (class phylo).

seaview_exec

a character string giving the path of the program.

Details

By default, the function assumes that the executable is installed in a directory located on the PATH. Alternatively the user can provide an absolute path to the executable (i.e. the location where the software was installed/uncompressed). This can be stored in the global options settings using options(bioseq.seaview.exec = "my_path_to_seaview").

References

Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.

Replace matched patterns in sequences

Description

Replace matched patterns in sequences

Usage

seq_replace_pattern(x, pattern, replacement)

Arguments

x

a DNA, RNA or AA vector.

pattern

a DNA, RNA or AA vectors (but same as x) or a character vector of regular expressions, or a list. See section Patterns.

replacement

a vector of replacements.

Value

A vector of same class as x.

Patterns

It is important to understand how patterns are treated in bioseq.

Patterns are recycled along the sequences (usually the x argument). This means that if a pattern (vector or list) is of length > 1, it will be replicated until it is the same length as x. The reverse is not true and a vector of patterns longer than a vector of sequences will raise a warning.

Patterns can be DNA, RNA or AA vectors (but they must be from the same class as the sequences they are matched against). If patterns are DNA, RNA or AA vectors, they are disambiguated prior to matching. For example pattern dna("ARG") will match AAG or AGG.

Alternatively, patterns can be a simple character vector containing regular expressions.

Vectors of patterns (DNA, RNA, AA or regex) can also be provided in a list. In that case, each vector of the list will be collapsed prior matching, which means that each vector element will be used as an alternative pattern. For example pattern list(c("AAA", "CCC"), "GG") will match AAA or CCC in the first sequence, GG in the second sequence, AAA or CCC in the third, and so on following the recycling rule.

@section Fuzzy matching: When max_error is greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Examples

x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
seq_replace_pattern(x, dna("AAA"), dna("GGGGGG"))
seq_replace_pattern(x, "^A.{2}T", "TTTTTT")

Cluster sequences by similarity

Description

Cluster sequences by similarity

Usage

seq_cluster(x, threshold = 0.05, method = "complete")

Arguments

x

a DNA, RNA or AA vector of sequences to clustered.

threshold

Threshold value (range in [0, 1]).

method

the clustering method (see details).

Details

The function uses ape dist.dna and dist.aa functions to compute pairwise distances among sequences and hclust for clustering.

Computing a full pairwise diastance matrix can be computationally expensive. It is recommended to use this function for moderate size dataset.

Supported methods are:

"single" (= Nearest Neighbour Clustering)
"complete" (= Farthest Neighbour Clustering)
"average" (= UPGMA)
"mcquitty" (= WPGMA)

Value

An integer vector with group memberships.

Examples


x <- c("-----TACGCAGTAAAAGCTACTGATG",
       "CGTCATACGCAGTAAAAACTACTGATG",
       "CTTCATACGCAGTAAAAACTACTGATG",
       "CTTCATATGCAGTAAAAACTACTGATG",
       "CTTCATACGCAGTAAAAACTACTGATG",
       "CGTCATACGCAGTAAAAGCTACTGATG",
       "CTTCATATGCAGTAAAAGCTACTGACG")
x <- dna(x)
seq_cluster(x)

Combine multiple sequences

Description

Combine multiple sequences

Usage

seq_combine(..., sep = "", collapse = NULL)

Arguments

...

One or more vectors of sequences (DNA, RNA, AA). They must all be of the same type. Short vectors are recycled.

sep

String to insert between input vectors.

collapse

If not NULL, combine everything with this string as separator.

Details

The strings sep and collapsew ill be coerced to the type of input vectors with a warning if some character have to replaced.

Value

A vector of sequences (if collapse is NULL). A vector with a single sequence, otherwise.

Examples


x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
y <- dna("TTTTTTTT", "AAAAAAAAA")
seq_combine(x, y)
seq_combine(y, x, sep = "CCCCC")
seq_combine(y, x, sep = "CCCCC", collapse = "GGGGG")

Find a consensus sequence for a set of sequences.

Description

Find a consensus sequence for a set of sequences.

Usage

seq_consensus(x, method = "chr_majority", weights = NULL, gaps = TRUE)

Arguments

x

a DNA, RNA or AA vector.

method

the consensus method (see Details).

weights

an optional numeric vector of same length as x giving a weight for each input sequence.

gaps

logical. Should the gaps ("-") taken into account.

Details

"chr_majority", "chr_ambiguity", "seq_centrality", "seq_majority"

For chr_ambiguity gap character always override other characters. Use gaps = FALSE to ignore gaps.

Value

A consensus sequence

Examples

x <- c("-----TACGCAGTAAAAGCTACTGATG",
       "CGTCATACGCAGTAAAAACTACTGATG",
       "CTTCATACGCAGTAAAAACTACTGATG",
       "CTTCATATGCAGTAAAAACTACTGATG",
       "CTTCATACGCAGTAAAAACTACTGATG",
       "CGTCATACGCAGTAAAAGCTACTGATG",
       "CTTCATATGCAGTAAAAGCTACTGACG")
x <- dna(x)
seq_consensus(x)

Count the number of matches in sequences

Description

Count the number of matches in sequences

Usage

seq_count_pattern(x, pattern)

Arguments

x

a DNA, RNA or AA vector.

pattern

a DNA, RNA or AA vectors (but same as x) or a character vector of regular expressions, or a list. See section Patterns.

Value

An integer vector.

Patterns

It is important to understand how patterns are treated in bioseq.

Alternatively, patterns can be a simple character vector containing regular expressions.

@section Fuzzy matching: When max_error is greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Examples


x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
seq_count_pattern(x, dna("AAA"))
seq_count_pattern(x, "T.G")

Crop sequences using delimiting patterns

Description

Crop sequences using delimiting patterns

Usage

seq_crop_pattern(
  x,
  pattern_in,
  pattern_out,
  max_error_in = 0,
  max_error_out = 0,
  include_patterns = TRUE
)

Arguments

x

a DNA, RNA or AA vector to be cropped.

pattern_in

patterns defining the beginning (left-side).

pattern_out

patterns defining the end (right-side).

max_error_in, max_error_out

numeric values ranging from 0 to 1 and giving the maximum error rate allowed between the target sequence and pattern_in/pattern_out. Error rate is relative to the length of the pattern.

include_patterns

logical. Should the matched pattern sequence included in the returned sequences?

Value

A cropped DNA, RNA or AA vector. Sequences where patterns are not detected returns NA.

Fuzzy matching

When max_error_in or max_error_out are greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Patterns

It is important to understand how patterns are treated in bioseq.

Alternatively, patterns can be a simple character vector containing regular expressions.

@section Fuzzy matching: When max_error is greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Examples


x <- dna("ACGTTAAAAAGTGTAGCCCCCGT", "CTCGAAATGA")
seq_crop_pattern(x, pattern_in = "AAAA", pattern_out = "CCCC")

Crop sequences between two positions

Description

Crop sequences between two positions

Usage

seq_crop_position(x, position_in = 1, position_out = -1)

Arguments

x

a DNA, RNA or AA vector.

position_in

an integer giving the position where to start cropping.

position_out

an integer giving the position where to stop cropping.

Value

A cropped DNA, RNA or AA vector.

Examples


x <- dna("ACGTTAGTGTAGCCGT")

# Drop the first 3 nucleotides (ACG)
seq_crop_position(x, position_in = 4)

# Crop codon between position 4 and 6
seq_crop_position(x, position_in = 4, position_out = 6)

Detect the presence of patterns in sequences

Description

Detect the presence of patterns in sequences

Usage

seq_detect_pattern(x, pattern, max_error = 0)

Arguments

x

a DNA, RNA or AA vector.

pattern

a DNA, RNA or AA vectors (but same as x) or a character vector of regular expressions, or a list. See section Patterns.

max_error

numeric value ranging from 0 to 1 and giving the maximum error rate allowed between the target sequence and the pattern. Error rate is relative to the length of the pattern.

Value

A logical vector.

Patterns

It is important to understand how patterns are treated in bioseq.

Alternatively, patterns can be a simple character vector containing regular expressions.

@section Fuzzy matching: When max_error is greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Examples


x <- dna(c("ACGTTAGTGTAGCCGT", "CTCGAAATGA"))
seq_detect_pattern(x, dna(c("CCG", "AAA")))

# Regular expression
seq_detect_pattern(x, "^A.{2}T")

# Fuzzy matching
seq_detect_pattern(x, dna("AGG"), max_error = 0.2)
# No match. The pattern has three character, the max_error
# has to be > 1/3 to allow one character difference.

seq_detect_pattern(x, dna("AGG"), max_error = 0.4)
# Match

Disambiguate biological sequences

Description

This function finds all the combinations of sequences corresponding to a given vector of sequences with ambiguities (IUPAC codes).

Usage

seq_disambiguate_IUPAC(x)

Arguments

x

a DNA, RNA or AA vector

Value

A list of DNA, RNA or AA vectors (depending on the input) giving all possible combinations.

Examples


x <- dna(c("AYCTGW", "CTTN"))
seq_disambiguate_IUPAC(x)

y <- seq_transcribe(x)
seq_disambiguate_IUPAC(y)

z <- aa("YJSNAALNX")
z <- seq_translate(y)
seq_disambiguate_IUPAC(z)

Extract matching patterns from sequences

Description

Extract matching patterns from sequences

Usage

seq_extract_pattern(x, pattern)

Arguments

x

a DNA, RNA or AA vector.

pattern

a DNA, RNA or AA vectors (but same as x) or a character vector of regular expressions, or a list. See section Patterns.

Value

A list of vectors of same class as x.

Patterns

It is important to understand how patterns are treated in bioseq.

Alternatively, patterns can be a simple character vector containing regular expressions.

@section Fuzzy matching: When max_error is greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Examples


x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
seq_extract_pattern(x, dna("AAA"))
seq_extract_pattern(x, "T.G")

Extract a region between two positions in sequences

Description

Extract a region between two positions in sequences

Usage

seq_extract_position(x, position_in, position_out)

Arguments

x

a DNA, RNA or AA vector.

position_in

an integer giving the position where to start to extract.

position_out

an integer giving the position where to stop to extract.

Value

A vector of same class as x.

Examples


x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
seq_extract_position(x, 3, 8)

Count the number of character in sequences

Description

Count the number of character in sequences

Usage

seq_nchar(x, gaps = TRUE)

Arguments

x

a DNA, RNA or AA vector.

gaps

if FALSE gaps are ignored.

Value

An integer vector giving the size of each sequence of x.

Examples


x <- dna(c("ATGCAGA", "GGR-----","TTGCCTAGKTGAACC"))
seq_nchar(x)
seq_nchar(x, gaps = FALSE)

Number of sequences in a vector

Description

This is an alias for length.

Usage

seq_nseq(x)

Arguments

x

a DNA, RNA or AA vector.

Value

an integer.

Remove matched patterns in sequences

Description

Remove matched patterns in sequences

Usage

seq_remove_pattern(x, pattern)

Arguments

x

a DNA, RNA or AA vector.

pattern

a DNA, RNA or AA vectors (but same as x) or a character vector of regular expressions, or a list. See section Patterns.

Value

A vector of same class as x.

Patterns

It is important to understand how patterns are treated in bioseq.

Alternatively, patterns can be a simple character vector containing regular expressions.

@section Fuzzy matching: When max_error is greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Examples


x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
seq_remove_pattern(x, dna("AAA"))
seq_remove_pattern(x, "^A.{2}T")

Remove a region between two positions in sequences.

Description

Remove a region between two positions in sequences.

Usage

seq_remove_position(x, position_in, position_out)

Arguments

x

a DNA, RNA or AA vector.

position_in

an integer giving the position where to start to remove.

position_out

an integer giving the position where to stop to remove.

Value

A vector of same class as x.

Examples


x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
seq_remove_position(x, 2, 6)
seq_remove_position(x, 1:2, 3:4)

Replace a region between two positions in sequences

Description

Replace a region between two positions in sequences

Usage

seq_replace_position(x, position_in, position_out, replacement)

Arguments

x

a DNA, RNA or AA vector.

position_in

an integer giving the position where to start to replace.

position_out

an integer giving the position where to stop to replace.

replacement

a vector of replacements.

Value

A vector of same class as x.

Examples


x <- dna("ACGTTAGTGTAGCCGT", "CTCGAAATGA")
seq_replace_position(x, c(5, 2), 6, "-------")

Reverse translate amino acid sequences

Description

The function perform reverse translation of amino acid sequences. Such operation does not exist in nature but is provided for completeness. Because of codon degeneracy it is expected to produce many ambiguous nucleotides.

Usage

seq_rev_translate(x, code = 1)

Arguments

x

an amino acid sequence (bioseq_aa)

code

an integer indicating the genetic code to use for reverse translation (default 1 uses the Standard genetic code). See Details.

Details

Gaps (-) are interpreted as unknown amino acids (X) but can be removed prior to the translation with the function seq_remove_gap.

Value

a vector of DNA sequences.

Examples


x <- dna("ACTTTGGCTAAG")
y <- seq_translate(x)
z <- seq_rev_translate(y)
z
# There is a loss of information during the reverse translation
all.equal(x, z)

Spell out sequences

Description

This function spells out nucleotides and amino acids in sequences.

Usage

seq_spellout(x, short = FALSE, collapse = " - ")

Arguments

x

a DNA, RNA or AA vector

short

logical. If TRUE, the function will return 3-letters short names for amino acids (ignored for DNA and RNA).

collapse

a character vector to separate the results. Set to NULL to avoid collapsing the results.

Value

A character vector if collapse is not NULL. A list of character vectors otherwise.

Examples

x <- dna("ACGT")
seq_spellout(x)

x <- rna("ACGU")
seq_spellout(x)

x <- aa("ACGBTX")
seq_spellout(x)

Split sequences into k-mers

Description

Split sequences into k-mers

Usage

seq_split_kmer(x, k)

Arguments

x

A DNA, RNA or AA vector.

k

an integer giving the size of the k-mer.

Value

a list of k-mer vectors of same class as x.

Examples


x <- dna(a ="ACGTTAGTGTAGCCGT", b = "CTCGAAATGA")
seq_split_kmer(x, k = 5)

Split sequences

Description

Split sequences

Usage

seq_split_pattern(x, pattern)

Arguments

x

a DNA, RNA or AA vector.

pattern

a DNA, RNA or AA vectors (but same as x) or a character vector of regular expressions, or a list. See section Patterns.

Value

A list of vectors of same class as x.

Patterns

It is important to understand how patterns are treated in bioseq.

Alternatively, patterns can be a simple character vector containing regular expressions.

@section Fuzzy matching: When max_error is greater than zero, the function perform fuzzy matching. Fuzzy matching does not support regular expression.

Examples


x <- dna(a = "ACGTTAGTGTAGCCGT", b = "CTCGAAATGA")
seq_split_pattern(x, dna("AAA"))
seq_split_pattern(x, "T.G")

Compute G+C content

Description

Compute G+C content

Usage

seq_stat_gc(x)

Arguments

x

a DNA or RNA

Details

Ambiguous characters (other than S and W) are ignored.

Value

A numeric vector of G+C proportions.

Examples


x <- dna(c("ATGCAGA", "GGR-----","TTGCCTAGKTGAACC"))

seq_stat_gc(x)

Compute proportions for characters

Description

Compute proportions for characters

Usage

seq_stat_prop(x, gaps = FALSE)

Arguments

x

a DNA, RNA or AA vector.

gaps

if FALSE gaps are ignored.

Value

A list of vectors indicating the proportion of characters in each sequence.

Examples


x <- dna(c("ATGCAGA", "GGR-----","TTGCCTAGKTGAACC"))
seq_stat_prop(x)
seq_stat_prop(x, gaps = TRUE)

Translate DNA/RNA sequences into amino acids

Description

Translate DNA/RNA sequences into amino acids

Usage

seq_translate(x, code = 1, codon_frame = 1, codon_init = FALSE)

Arguments

x

a vector of DNA (bioseq_dna) or RNA (bioseq_rna).

code

an integer indicating the genetic code to use for translation (default 1 uses the Standard genetic code). See Details.

codon_frame

an integer giving the nucleotide position where to start translation.

codon_init

a logical indicating whether the first codon is evaluated as a possible codon start and translated to methionine.

Details

Several genetic codes can be used for translation. See genetic-codes to get the list of available genetic codes and their ID number.

Gaps (-) are interpreted as unknown nucleotides (N) but can be removed prior to the translation with the function seq_remove_gap.

The function deals with ambiguities on both sides. This means that if ambiguous codons cannot be translated to amino acid, they are translated to the most specific ambiguous amino acids (X in the most extreme case).

Value

An amino acid vector (bioseq_aa).

Examples

x <- dna(c("ATGCAGA", "GGR","TTGCCTAGKTGAACC", "AGGNGC", "NNN"))
seq_translate(x)

Transcribe DNA, reverse-transcribe RNA

Description

Transcribe DNA, reverse-transcribe RNA

Usage

seq_transcribe(x)

seq_rev_transcribe(x)

Arguments

x

A vector of DNA for seq_transcribe, a vector of RNA for seq_rev_transcribe

Value

A vector of RNA for seq_transcribe, a vector of DNA for seq_rev_transcribe

Sequence validator

Description

Validate character strings before sequence construction.

Usage

validate_seq(x, alphabet, invalid_replacement, type = "DNA")

Arguments

x

a character vector.

alphabet

a character vector defining the sequence alphabet;

invalid_replacement

a character to replace non valid characters

type

type of sequence ("DNA", "RNA", "AA"). It is only used to provide more informative warning messages.

Details

Validation steps:

Check that x is a character vector, fails if not.
Force alpha characters to uppercase
Delete blank characters (spaces and tabs)
Delete line breaks
Converts . (dots) to - (as both can represent a gap)
Replace invalid characters with N/X (with a warning).

Value

A character vector.

Internal

Description

Internal

Usage

## S3 method for class 'bioseq_aa'
vec_ptype2(x, y, ...)

## S3 method for class 'bioseq_aa'
vec_cast(x, to, ...)

## S3 method for class 'bioseq_dna'
vec_ptype2(x, y, ...)

## S3 method for class 'bioseq_dna'
vec_cast(x, to, ...)

## S3 method for class 'bioseq_rna'
vec_ptype2(x, y, ...)

## S3 method for class 'bioseq_rna'
vec_cast(x, to, ...)

Arguments

x

an object.

y

an object.

...

other arguments.

to

a class

Write sequences in FASTA format

Description

Write sequences in FASTA format

Usage

write_fasta(x, file, append = FALSE, line_length = 80, block_length = 10)

Arguments

x

a DNA, RNA or AA vector.

file

a path to a file or a connection.

append

a logical. If TRUE append the data to the file. If FALSE (default), overwrite the file.

line_length

length (in number of character) of one line (excluding spaces separating blocks). Use Inf to avoid line breaks.

block_length

length (in number of character) of one block. Use the same value as line_length or Inf to avoid block separation.

bioseq: A Toolbox for Manipulating Biological Sequences

Description

Author(s)

See Also

Build an amino acid (AA) vector

Description

Usage

Arguments

Value

See Also

Examples

AliView: DNA sequences viewer

Description

Usage

Arguments

Details

References

See Also

Biological alphabets

Description

DNA

RNA

AA

References

Convert DNAbin/AAbin to tibble

Description

Usage

Arguments

Value

See Also

Examples

Convert bioseq DNA, RNA and AA to tibble

Description

Usage

Arguments

Value

See Also

Examples

Coerce to AAbin

Description

Usage

Arguments

Value

See Also

Coerce tibble to AAbin

Description

Usage

Arguments

Value

Coerce to DNAbin

Description

Usage

Arguments

Value

See Also

Coerce tibble to DNAbin

Description

Usage

Arguments

Value

Coercion to an amino acid (AA) vector

Description

Usage

Arguments

Value

See Also

Coercion to DNA vector

Description

Usage

Arguments

Value

See Also

Coercion to RNA vector

Description

Usage

Arguments

Value

See Also

Coerce to seqinr alignment

Description