MEET (version 5.1.1)

CalculScores: Calcul Score of a Sequence, using a loggods matrix

Description

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)

Usage

CalculScores(sequencia, logodds)

Arguments

sequencia

Sequence to analyze

logodds

logodds matrix for a given motif.

Value

score: score of the studied sequence

References

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

See Also

CalculPSSM, CalculInformation

Examples

require("MEET")
#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)