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

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

View source: R/CalculScores.R

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

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CalculScores(sequencia, logodds)

Arguments

sequencia

Sequence to analyze

logodds

logodds matrix for a given motif.

Value

score: score of the studied sequence

Author(s)

Erola Pairo <epairo@ibecbarcelona.eu>

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

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#
#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)
  

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