transform: Convert biological sequences into binary code

In seq2R: Simple Method to Detect Compositional Changes in Genomic Sequences

Convert biological sequences into binary code

Description

Biological sequences are categorical variables. With this function the four nucleotides are coded with two bits, 0 and 1 (binary numeral system) for being used by almost all modern computers.

Usage

transform(x)

Arguments

x	The object obtained with read.all or read.genbank functions is the argument required for transform. The nature of the sequence is DNA. Sequences are returned as a vector of single characters.

Value

The returned list has two component ($AT, $CG). Both of them containing a matrix with values about their critical points (maximum and minimum), and their lower and upper 95% confidence intervals.

AT	Variable A and T with binary system.
CG	Variable C and G with binary system.

Author(s)

Nora M. Villanueva and Marta Sestelo.

Examples

library(seq2R)

#mtDNAhum <- read.genbank("NC_012920")
data(mtDNAhum)
DNA <- transform(mtDNAhum)
DNA

seq2R documentation built on Sept. 30, 2024, 5:06 p.m.