MEET-package: MEET: Motif Elements Estimation Toolkit

Description Arguments Details Author(s) Examples

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 <[email protected]> and Joan Maynou <[email protected]>

Examples

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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')

MEET documentation built on May 31, 2017, 4:10 a.m.