tidysq (version 1.2.3)

collapse: Collapse multiple sequences into one

Description

Joins sequences from a vector into a single sequence. Sequence type remains unchanged.

Usage

collapse(x, ...)
# S3 method for sq
collapse(x, ..., NA_letter = getOption("tidysq_NA_letter"))

Value

sq object of the same type as input but with exactly one sequence.

Arguments

x

[sq]
An object this function is applied to.

...

further arguments to be passed from or to other methods.

NA_letter

[character(1)]
A string that is used to interpret and display NA value in the context of sq class. Default value equals to "!".

Details

collapse() joins sequences from supplied sq object in the same order as they appear in said vector. That is, if there are three sequences AGGCT, ATCCGT and GAACGT, then resulting sequence will be AGGCTATCCGTGAACGT. This operation does not alter the type of the input object nor its alphabet.

See Also

Functions that affect order of elements: bite(), paste(), reverse()

Examples

# Creating objects to work on:
sq_ami <- sq(c("MIAANYTWIL","TIAALGNIIYRAIE", "NYERTGHLI", "MAYXXXIALN"),
             alphabet = "ami_ext")
sq_dna <- sq(c("ATGCAGGA", "GACCGAACGAN", ""), alphabet = "dna_ext")
sq_unt <- sq(c("ATGCAGGA?", "TGACGAGCTTA", "", "TIAALGNIIYRAIE"))

# Collapsing sequences:
collapse(sq_ami)
collapse(sq_dna)
collapse(sq_unt)

# Empty sq objects are collapsed as well (into empty string - ""):
sq_empty <- sq(character(), alphabet = "rna_bsc")
collapse(sq_empty)