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

Value

score: score of the studied sequence

Author(s)

Erola Pairo <epeiroatibec.pcb.ub.es>

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)
  

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MEET)
Loading required package: seqinr
Loading required package: pcaMethods
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'pcaMethods'

The following object is masked from 'package:stats':

    loadings

Loading required package: Matrix
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:Biobase':

    combine, contents

The following object is masked from 'package:BiocGenerics':

    combine

The following object is masked from 'package:seqinr':

    translate

The following objects are masked from 'package:base':

    format.pval, round.POSIXt, trunc.POSIXt, units

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: seqLogo
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MEET/CalculScores.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CalculScores
> ### Title: Calcul Score of a Sequence, using a loggods matrix
> ### Aliases: CalculScores
> 
> ### ** Examples
> 
> require("MEET")
> #First example, calculating logodds of a Sequence 
> data(TFlogodds)
> data(Sequence)
> CalculScores(sequencia=Sequence, logodds=TFlogodds)
[1] 39.37294
> #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)
[1] 35.97108
>   
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>