MEDMat: Minimum Entropy Decomposition
In aramette/otu2ot: Calculate oligotypes for aligned FASTA sequences

Description Usage Arguments Value Note Author(s) References Examples

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

1	MEDMat(AlignedSequences=Sequences, minseq = 21, entropymin = 0.6, Plot = TRUE)

`AlignedSequences`	matrix. Sequence Id-by-position matrix as produced by e.g. ImportFastaAlignmentImportFastaAlignment(). This is the main difference to MED(), the latter working on files and not on object in the current workspace.
`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.

A matrix of sequence ids (rows) by oligotypes.

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).

Alban Ramette

Inspired by M. Eren et al. paper.

## File is stored in the current working directory.
#File="HGB_0013_GXJPMPL01A3OQX.fasta"
Aln.list<- ImportFastaAlignment(File) #path to FASTA file
Names <-  Aln.list[[1]]
Sequences <- toupper(Aln.list[[2]])# do not trim trailing dots at 5' and 3' ends

OT.seq.concat <- MEDMat( 
	    AlignedSequences=Sequences,  
             minseq=21,
             entropymin=0.6,
             Plot=TRUE
)