MED: Minimum Entropy Decomposition

In aramette/otu2ot: Calculate oligotypes for aligned FASTA sequences

Description

Decompose a set of aligned FASTA sequences until either the minimum entropy threshold or the minumum number of sequences in all subalignments are reached.

Usage

MED(File = "E:\Oligotyping\OT.180OTU_fasta\arbTrimmedFASTAsForOligotyping\HGB_0013_GXJPMPL01A3OQX.fasta", minseq = 21, entropymin = 0.6, Plot = TRUE)

Arguments

File	character. path to file.
minseq	numeric. minimum number of sequences before the procedure stops for a specific subalignment.
entropymin	numeric. minimum entropy level before the procedure stops for a specific subalignment.
Plot	logical. Plots the entropy profiles and also the base composition for the identified high entropy positions.

Value

A matrix of sequence ids (rows) by oligotypes.

Note

The procedure currently only takes one component, which corresponds to the highest entropy. In case of ties, it will take the first site in the list (i.e. smallest site position).

Author(s)

Alban Ramette

References

Inspired by M. Eren et al. paper.

Examples

## The File is stored in the current working directory.
OT.seq.concat <- MED(File="mock-env-aligned.fasta",minseq=21,entropymin=0.6,Plot=FALSE)

aramette/otu2ot documentation built on May 10, 2019, 12:46 p.m.