CalculSimilarity: Similarity Score between a Sequence and a PSSM model

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

View source: R/CalculSimilarity.R

Description

The Similarity between a Sequence and a PSSM model is calculated using the score of the Sequence, and the minimum and maximum scores that can be obtained with the model. As the score approaches to 1, the sequence is more likely to belong to the modeled motif

Usage

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CalculSimilarity(current, minim, maxim)

Arguments

current

Score of the studied sequence

minim

minimum score obtained using the PSSM model

maxim

maximum score obtained using the PSSM model

Value

similarity: between 0 and 1, similarity of the given sequence to the model

Author(s)

Erola Pairo <epairo@ibecbarcelona.eu>

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

CalculScores

Examples

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data(TFlogodds)
data(BackgroundOrganism)
data(Sequence)
current<-CalculScores(Sequence, TFlogodds)

maxim<-0
minim<-0

for(j in 1:dim(TFlogodds)[1]){
	  minim <- min(TFlogodds[j,])+minim
	  maxim <- max(TFlogodds[j,])+maxim
	  }
Similarity<-CalculSimilarity(current, minim, maxim)
  

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