Package 'bioseq'

Description

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

Usage

aa(...)

Arguments

Value

vector of class bioseq_aa

See Also

Other classes: dna(), rna()

Examples

aa("AGGTGC", "TTCGA")

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

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

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

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.

See Also

Other GUI wrappers: seaview()

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.

Description

Coercion to an amino acid (AA) vector

Usage

as_aa(x)

Arguments

Value

An amino acid vector of class bioseq_aa

See Also

Other conversions: as-tibble-ape, as-tibble-bioseq, as_AAbin(), as_DNAbin(), as_dna(), as_rna(), as_seqinr_alignment()

Description

Coerce to AAbin

Usage

as_AAbin(x, ...)

Arguments

Value

An AAbin object.

See Also

Other conversions: as-tibble-ape, as-tibble-bioseq, as_DNAbin(), as_aa(), as_dna(), as_rna(), as_seqinr_alignment()

Description

Coerce tibble to AAbin

Usage

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

Arguments

Value

An AAbin object.

Description

Coercion to DNA vector

Usage

as_dna(x)

Arguments

Value

A DNA vector of class bioseq_dna

See Also

Other conversions: as-tibble-ape, as-tibble-bioseq, as_AAbin(), as_DNAbin(), as_aa(), as_rna(), as_seqinr_alignment()

Description

Coerce to DNAbin

Usage

as_DNAbin(x, ...)

Arguments

Value

A DNAbin object.

See Also

Other conversions: as-tibble-ape, as-tibble-bioseq, as_AAbin(), as_aa(), as_dna(), as_rna(), as_seqinr_alignment()

Description

Coerce tibble to DNAbin

Usage

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

Arguments

Value

A DNAbin object.

Description

Coercion to RNA vector

Usage

as_rna(x)

Arguments

Value

A RNA vector of class bioseq_rna

See Also

Other conversions: as-tibble-ape, as-tibble-bioseq, as_AAbin(), as_DNAbin(), as_aa(), as_dna(), as_seqinr_alignment()

Description

Coerce to seqinr alignment

Usage

as_seqinr_alignment(x, ...)

Arguments

Value

An alignment object.

See Also

Other conversions: as-tibble-ape, as-tibble-bioseq, as_AAbin(), as_DNAbin(), as_aa(), as_dna(), as_rna()

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

Value

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

See Also

Other conversions: as-tibble-bioseq, as_AAbin(), as_DNAbin(), as_aa(), as_dna(), as_rna(), as_seqinr_alignment()

Examples

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

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

Value

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

See Also

Other conversions: as-tibble-ape, as_AAbin(), as_DNAbin(), as_aa(), as_dna(), as_rna(), as_seqinr_alignment()

Examples

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

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.

Description

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

Usage

dna(...)

Arguments

Value

a vector of class bioseq_dna

See Also

Other classes: aa(), rna()

Examples

dna("AGGTGC", "TTCGA")

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

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

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"

See Also

read_fasta to parse these data.

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

Description

This function returns TRUE for objects of class bioseq_aa

Usage

is_aa(x)

Arguments

Value

Logical.

Examples

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

Description

This function returns TRUE for objects of class bioseq_dna

Usage

is_dna(x)

Arguments

Value

Logical.

Examples

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

Description

This function returns TRUE for objects of class bioseq_rna

Usage

is_rna(x)

Arguments

Value

Logical.

Examples

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

Description

Amino acid (AA) vector constructor

Usage

new_aa(x = character())

Arguments

Description

DNA vector constructor

Usage

new_dna(x = character())

Arguments

Description

RNA vector constructor

Usage

new_rna(x = character())

Arguments

Description

Read sequences in FASTA format

Usage

read_fasta(file, type = "DNA")

Arguments

Value

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

See Also

Other input/output operations: write_fasta()

Description

Reverse and complement sequences

Usage

seq_complement(x)

seq_reverse(x)

Arguments

Value

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

See Also

Other biological operations: seq_rev_translate(), seq_translate(), transcription

Examples

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

Description

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

Usage

rna(...)

Arguments

Value

a vector of class bioseq_rna

See Also

Other classes: aa(), dna()

Examples

rna("AGGUGC", "UUCGA")

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

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

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

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.

See Also

Other GUI wrappers: aliview()

Description

Cluster sequences by similarity

Usage

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

Arguments

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.

See Also

Function seq_consensus to compute consensus and representative sequences for clusters.

Other aggregation operations: seq_consensus()

Examples

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

Description

Combine multiple sequences

Usage

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

Arguments

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.

See Also

stri_join from stringi and str_c from stringr for the underlying implementation.

Other string operations: seq-replace, seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

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")

Description

Find a consensus sequence for a set of sequences.

Usage

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

Arguments

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

See Also

Other aggregation operations: seq_cluster()

Examples

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

Description

Count the number of matches in sequences

Usage

seq_count_pattern(x, pattern)

Arguments

Value

An integer vector.

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.

See Also

stri_count from stringi and str_count from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

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

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.

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.

See Also

stri_extract from stringi, str_extract from stringr and afind from stringdist for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

Description

Crop sequences between two positions

Usage

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

Arguments

Value

A cropped DNA, RNA or AA vector.

See Also

stri_sub from stringi and str_sub from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

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)

Description

Detect the presence of patterns in sequences

Usage

seq_detect_pattern(x, pattern, max_error = 0)

Arguments

Value

A logical vector.

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.

See Also

stri_detect from stringi, str_detect from stringr and afind from stringdist for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

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

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

Value

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

See Also

Other op-misc: seq_nchar(), seq_nseq(), seq_spellout(), seq_stat_gc(), seq_stat_prop()

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)

Description

Extract matching patterns from sequences

Usage

seq_extract_pattern(x, pattern)

Arguments

Value

A list of vectors 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.

See Also

stri_extract from stringi and str_extract from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

Description

Extract a region between two positions in sequences

Usage

seq_extract_position(x, position_in, position_out)

Arguments

Value

A vector of same class as x.

See Also

stri_extract from stringi and str_extract from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

Description

Count the number of character in sequences

Usage

seq_nchar(x, gaps = TRUE)

Arguments

Value

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

See Also

Other op-misc: seq_disambiguate_IUPAC(), seq_nseq(), seq_spellout(), seq_stat_gc(), seq_stat_prop()

Examples

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

Description

This is an alias for length.

Usage

seq_nseq(x)

Arguments

Value

an integer.

See Also

Other op-misc: seq_disambiguate_IUPAC(), seq_nchar(), seq_spellout(), seq_stat_gc(), seq_stat_prop()

Description

Remove matched patterns in sequences

Usage

seq_remove_pattern(x, pattern)

Arguments

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.

See Also

str_remove from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

Description

Remove a region between two positions in sequences.

Usage

seq_remove_position(x, position_in, position_out)

Arguments

Value

A vector of same class as x.

See Also

str_remove from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

Description

Replace a region between two positions in sequences

Usage

seq_replace_position(x, position_in, position_out, replacement)

Arguments

Value

A vector of same class as x.

See Also

stri_replace from stringi and str_replace from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

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

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.

See Also

Other biological operations: rev_complement, seq_translate(), transcription

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)

Description

This function spells out nucleotides and amino acids in sequences.

Usage

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

Arguments

Value

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

See Also

Other op-misc: seq_disambiguate_IUPAC(), seq_nchar(), seq_nseq(), seq_stat_gc(), seq_stat_prop()

Examples

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

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

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

Description

Split sequences into k-mers

Usage

seq_split_kmer(x, k)

Arguments

Value

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

See Also

seq_split_pattern.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_pattern()

Examples

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

Description

Split sequences

Usage

seq_split_pattern(x, pattern)

Arguments

Value

A list of vectors 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.

See Also

stri_split from stringi and str_split from stringr for the underlying implementation.

Other string operations: seq-replace, seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer()

Examples

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

Description

Compute G+C content

Usage

seq_stat_gc(x)

Arguments

Details

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

Value

A numeric vector of G+C proportions.

See Also

Other op-misc: seq_disambiguate_IUPAC(), seq_nchar(), seq_nseq(), seq_spellout(), seq_stat_prop()

Examples

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

seq_stat_gc(x)

Description

Compute proportions for characters

Usage

seq_stat_prop(x, gaps = FALSE)

Arguments

Value

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

See Also

Other op-misc: seq_disambiguate_IUPAC(), seq_nchar(), seq_nseq(), seq_spellout(), seq_stat_gc()

Examples

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

Description

Translate DNA/RNA sequences into amino acids

Usage

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

Arguments

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).

See Also

Other biological operations: rev_complement, seq_rev_translate(), transcription

Examples

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

Description

Replace matched patterns in sequences

Usage

seq_replace_pattern(x, pattern, replacement)

Arguments

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.

See Also

stri_replace from stringi and str_replace from stringr for the underlying implementation.

Other string operations: seq_combine(), seq_count_pattern(), seq_crop_pattern(), seq_crop_position(), seq_detect_pattern(), seq_extract_pattern(), seq_extract_position(), seq_remove_pattern(), seq_remove_position(), seq_replace_position(), seq_split_kmer(), seq_split_pattern()

Examples

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

Description

Transcribe DNA, reverse-transcribe RNA

Usage

seq_transcribe(x)

seq_rev_transcribe(x)

Arguments

Value

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

See Also

Other biological operations: rev_complement, seq_rev_translate(), seq_translate()

Description

Write sequences in FASTA format

Usage

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

Arguments

See Also

Other input/output operations: read_fasta()