ModelMATCH: Match algorithm to detect TFBS in a sequence

In MEET: MEET: Motif Elements Estimation Toolkit

Description

Match algorithm is used to construct a PWM model of the intput TFBS sequences. The returned values are the PWM model and the parameters needed to predict using MATCH and the PWM, as the position of the Core, the minimum and maximum scores for a query sequence and its core, the Corecut parameter and the dimensions of teh TFBS matrix.

Usage

ModelMATCH(iicc)

Arguments

iicc	options of the MEET program

Details

The specific parameters for this detection are: the transcription factor to model and the background probabilities for each nucleotide

Value

output: a list with the model and the parameters

model	logodds matrix using information per site
parametersModel	posCore=position of the core, minim_core=minimum score for the core, maxim_core= maximum score for the core, minim=minimu score, maxim=maximum score, Corecut= percentage of core score that we want to consider, core=logodds for the core, ncolTFBS=dimension of the TFBS matrix

Author(s)

Erola Pairo <[e-mail]>

References

E. Kel , E. Gossling , I. Reuter , E. Cheremushkin , O.V. Kel-Margoulis , and E. Wingender MATCHTM: a tool for searching transcription factor binding sites in DNA sequences Nucl. Acids Res. 31: 3576-3579.

See Also

MEET, kfold.MATCH, ModelPCA

Examples

data(iicc)
data(TranscriptionFactor)
iicc$method<-"MATCH"
iicc$pvalor<-0.8
iicc$parameter<-60
ModelMATCH(iicc)

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