kfold.MATCH: MATCH validation process

In MEET: MEET: Motif Elements Estimation Toolkit

Description

For a vector of Core cut values this function calculates returns a matrix of Similarities and labels indicating if a sequence position is a binding site or not. To calculate the Similartiy a leave-one-out cross validation model is used. With the utput of this function a ROC curve can be calculated for each Core Similarity and the results can be compared.

Usage

kfold.MATCH(iicc, Seqin)

Arguments

iicc	List of options described in the MEET program
Seqin	DNA sequence

Author(s)

Erola Pairo <epeiroatibec.pcb.ub.es>

References

A.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

Match, MEET

Examples

require("MEET")
require("seqinr")
data(iicc)
data(TranscriptionFactor)
pathMEET <- system.file("sequences", package = "MEET")
iicc$method<-"MATCH"
iicc$vector<-c(0.5, 0.8)
kfold.MATCH(iicc, Seqin = paste(pathMEET, "AP1.fa", sep = "/"))

MEET documentation built on May 2, 2019, 1:45 p.m.