seq_spellout {bioseq}

R Documentation

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.

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)

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