seqFormat-methods: Process the multiple sequence alignment files

In CorMut: Detect the correlated mutations based on selection pressure

Description

Process the multiple sequence alignment files, the results can be used for the other functional functions. Note that the reference sequence should be included as the first sequence.

Usage

seqFormat(x, format = c("clustal","fasta","mase","phylip","msf"))

Arguments

x	multiple sequence alignment files
format	a character string specifying the format of the file: "clustal","fasta","mase","phylip","msf", refer to read.alignment function in seqinr package for details.

Value

A vector of sequences with names is returned.

Note

To ensure an exact result, the reference sequence should be included in the alignment as the first sequence.

Author(s)

Zhenpeng Li

Examples

examplefile=system.file("extdata","PI_treatment.aln",package="CorMut")
example=seqFormat(examplefile)

Example output

Loading required package: seqinr
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

CorMut documentation built on April 28, 2020, 7:09 p.m.