as.alignment: Constructor for class alignment

In seqinr: Biological Sequences Retrieval and Analysis

Constructor for class alignment

Description

Returns an object of (S3) class alignment.

Usage

as.alignment(nb = NULL, nam = NULL, seq = NULL, com = NULL)

Arguments

nb	integer. The number of sequences in the alignment.
nam	vector of nb character strings. The sequence names.
seq	vector of nb character strings. The aligned sequences.
com	vector of nb character strings. The comments about sequences.

Value

An object of class alignment which is a list with the following components:

nb	the number of aligned sequences
nam	a vector of strings containing the names of the aligned sequences
seq	a vector of strings containing the aligned sequences
com	a vector of strings containing the commentaries for each sequence or NA if there are no comments

Author(s)

D. Charif, J.R. Lobry

References

citation("seqinr")

See Also

read.alignment, as.matrix.alignment, read.fasta, write.fasta, reverse.align, dist.alignment.

Examples

as.alignment(nb = 2, nam = c("one", "two"), 
  seq = c("-ACGT", "GACG-"), com = c("un", "deux"))

seqinr documentation built on March 31, 2023, 3:05 p.m.