CalculScores: Calcul Score of a Sequence, using a loggods matrix
In MEET: MEET: Motif Elements Estimation Toolkit

Description Usage Arguments Value Author(s) References See Also Examples

Giving a logodds matrix, the Score of a sequence is calculated as the sum of the logodds of each nucleotide at each position of the sequence (equivalent to calculating the probability of each nucleotide at each position)

1	CalculScores(sequencia, logodds)

`sequencia`	Sequence to analyze
`logodds`	logodds matrix for a given motif.

score: score of the studied sequence

Erola Pairo <epairo@ibecbarcelona.eu>

Gary D. Stormo. DNA binding sites: representation and discovery. Bioinformatics (2000) 16(1): 16-23 doi:10.1093/bioinformatics/16.1.16

CalculPSSM, CalculInformation

#
#First example, calculating logodds of a Sequence 
data(TFlogodds)
data(Sequence)
CalculScores(sequencia=Sequence, logodds=TFlogodds)
#
#given a Transfac matrix, calculate first loggods and then scores
data(TranscriptionFactor)
data(BackgroundOrganism)
data(Sequence)
Factortrans<-TranscriptionFactor
suma<-apply(Factortrans,2,function(y){sum(y=="-")})
Factortrans<-Factortrans[, suma==0]
logodds<-CalculInformation(matriu=Factortrans, Prob=Prob)
logodds <- logodds[,2:dim(logodds)[2]]
CalculScores(sequencia=Sequence,logodds=logodds)