MEET: MEET: Motif Elements Estimation Toolkit
In MEET: MEET: Motif Elements Estimation Toolkit

Description Usage Arguments Details Examples

MEET (Motif Elements Estimation Toolkit) is a R-package that integrates a set of computational algorithms for the detection of Transcription Factor Binding Sites (TFBS)

1	MEET(TF,nameTF, seqin, alg, method,mode, org, vector, num_motif, len_motif, direction, threshold, order, model,position, mv, gapopen, maxiters, gapextend,optionsFile)

`TF`	A set of nucleotide sequences
`nameTF`	Transcription Factor name
`seqin`	Candidate sequence
`alg`	A set of Multiple Sequence Alignment
`method`	A set of motif discovery algorithms
`mode`	Training or detection
`org`	Background organism
`vector`	Characteristic parameters methodfor leave-one-out cross-training.
`num_motif`	Number of motif
`len_motif`	Length of motif
`direction`	Forward, reverse or both
`threshold`	P-value
`order`	Renyi Order
`model`	model
`position`	Binding site position for training
`mv`	missing values
`gapopen`	The gap open score
`maxiters`	Maximum number of iterations
`gapextend`	The gap extend score
`optionsFile`	Path for MEME/MAST, clustalx and muscle

This function need the next packages: seqinr, fields, pcaMethods, Matrix, ROCR, Hmisc, KernSmooth. Moreover, it needs the next software: MEME/MAST Version 4.4.0, MATCH Version 1.0, MDscan, ClustalW and Muscle Version 3.8.

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library(MEET)
pathMEET<-system.file("exdata",package="MEET")
Detection<-MEET(org="Drosophila melanogaster",nameTF="a1",seqin=paste(pathMEET,"DNAmeet.afa",sep="/"),method="Divergence",mode="detection",threshold=0.001,optionsFile='.optionsmeet')