phyclust (version 0.1-30)

file.read: Read Data from Files by Formats and Return a seq.data Object

Description

Two major file formats are supported in phyclust, Format phylip and Format fasta. These functions only read files in basic syntax, and return an object in Class seq.data.

Usage

read.fasta(filename, byrow = TRUE, code.type = .code.type[1], aligned = TRUE,
           sep = "")
read.fasta.format(filename, byrow = TRUE, aligned = TRUE, sep = "")
read.phylip(filename, byrow = TRUE, code.type = .code.type[1], sep = "")
read.phylip.format(filename, byrow = TRUE, sep = "")

Value

Return an object in Class seq.data.

Arguments

filename

a file name where data is read from.

byrow

advanced option, default = TRUE.

code.type

either "NUCLEOTIDE" (default) or "SNP".

aligned

indicate aligned data.

sep

use to split sites, "" (default) and "," for "CODON".

Author

Wei-Chen Chen

Details

For unaligned sequences, read.fasta returns a list storing data. read.phylip is only for aligned data and returns a matrix.

read.fasta.format and read.phylip.format will read in original coding without any transformation as code.type = NULL in write.fasta and write.phylip. Suppose these functions return an object ret, one can write other functions ret2aa() to post transform the coding and replace ret$org by the results of ret2aa(ret$org.code).

byrow indicates the data will be store by row or not. Usually, the default is TRUE. The FALSE is only for advance users with careful manipulations and for speeding up the bootstraps.

sep can specify a character which is used to split sites in file. By default, "" denote no character between sites. Only "CODON" id requires a character to avoid ambiguity

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

See Also

write.fasta, write.phylip.

Examples

if (FALSE) {
library(phyclust, quiet = TRUE)

# PHYLIP
data.path <- paste(.libPaths()[1], "/phyclust/data/crohn.phy", sep = "")
(my.snp <- read.phylip(data.path, code.type = "SNP"))

# FASTA
data.path <- paste(.libPaths()[1], "/phyclust/data/pony625.fas", sep = "")
(my.pony <- read.fasta(data.path))
}