consensus: consensus

In GuangchuangYu/seqmagick: Sequence Manipulation Utilities

consensus

Description

consensus of aligned sequences

consensus of aligned sequences

Usage

consensus(x, type = "DNA")

bs_consensus(x, type = "DNA", r = 1)

Arguments

x	BStringSet object
type	currently, only DNA supported
r	if any NT > r, it will be selected as representative base

Value

consensus sequence string

consensus sequence string

Author(s)

Guangchuang Yu

Examples

## Not run: 
fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
## align first 5 sequences, use `bs_aln(x)` to align all sequences
aln <- bs_aln(x[1:5])
## or bs_consensus(aln)
consensus(aln)

## End(Not run)

GuangchuangYu/seqmagick documentation built on Feb. 9, 2024, 3:06 a.m.