IUPAC_Boolean: IUPAC_boolean

In brengong/ConservationtextmineR:

Description

Converts IUPAC coded DNA sequences to a boolean syntax that can be utilized in query searches.

Usage

IUPAC_Boolean(DNAseq, stringency)

Arguments

DNAseq	a vector of DNA characters in IUPAC code.
stringency	a character designating "high", "medium", or "low" stringency levels.

Details

Requires a vector of DNA characters in IUPAC code.

There are three different stringency levels: high, medium, and low. The high stringency substitutes all IUPAC symbols for their nucleotide designations. Medium stringency substitutes IUPAC symbols with one and two nucleotide designations while treating those with three nucleotide designations as any nucleotide. High stringency retains only IUPAC symbols with one nucleotide designation while treating all others as any nucleotide.

Value

A vector of DNA characters converted to boolean syntax.

Author(s)

Brendan Gongol

Examples

sequences <- c("RTSWKMBDHVNATAATCGCTCCATACCTACATCN", "ATAGNNNCTCGACATWKMBACATCGCTACANNTACATAC")
IUPAC_Boolean(sequences, stringency = "high")
IUPAC_Boolean(sequences, stringency = "medium")
IUPAC_Boolean(sequences, stringency = "low")

brengong/ConservationtextmineR documentation built on July 29, 2019, 10:05 a.m.