MEET-package: MEET: Motif Elements Estimation Toolkit

In MEET: MEET: Motif Elements Estimation Toolkit

Description

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).

Arguments

TF	A set of nucleotide sequences
seqin	Candidate sequence
alg	A set of Multiple Sequence Alignment
method	A set of motif discovery algorithms
system	Training or detection
org	Background organism
vector	A set of Renyi Order (ITEME method) for 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
position	Binding site position for training
mv	missing values
gapopen	The gap open score
maxiters	Maximum number of iterations
gapextend	The gap extend score

Details

Package:	MEET
Type:	Package
Version:	1.0
Date:	2010-08-20
License:	GPL(>=2)
LazyLoad:	yes

Author(s)

Erola Pairo <[e-mail]> and Joan Maynou <[e-mail]>

Examples

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')

MEET documentation built on May 2, 2019, 5:52 p.m.