Information content in each position of a set of aligned DNA sequences

Description

Using as an input the set of aligned DNA sequences, information content in each position is calculated, taking into account background probability for each nucleotide. The first row of the returned sequence is the information in each postion, and the others are the loggods matrix.

Usage

CalculInformation(matriu, Prob)

Arguments

Value

matriu is a matrix with a first row that is the information content in each position and the next ones the logodds matrix using information content.

Author(s)

Erola Pairo <epeiroatibec.pcb.ub.es>

See Also

kfold.MATCH, CalculScores

Examples

data(TranscriptionFactor)
data(BackgroundOrganism)
CalculInformation(matriu=TranscriptionFactor, Prob=Prob)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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/CalculInformation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CalculInformation
> ### Title: Information content in each position of a set of aligned DNA
> ###   sequences
> ### Aliases: CalculInformation
> 
> ### ** Examples
> 
> data(TranscriptionFactor)
> data(BackgroundOrganism)
> CalculInformation(matriu=TranscriptionFactor, Prob=Prob)
            [,1]       [,2]       [,3]       [,4]        [,5]
 [1,] 0.61964852 0.02950707 0.85939349 1.50486070  0.35736343
 [2,] 0.86344137 0.04111626 0.42658115 2.78219995  1.18323446
 [3,] 0.37935306 0.13096713 0.52612656 0.82092805  0.11842238
 [4,] 1.17879638 3.38903959 0.23154929 0.05613316  0.05613316
 [5,] 1.40244795 0.06678324 4.24073547 0.06678324  0.06678324
 [6,] 1.40244795 0.06678324 4.24073547 0.06678324  0.06678324
 [7,] 2.15060117 0.10240958 0.10240958 0.10240958 11.48125177
 [8,] 1.40244795 0.06678324 4.24073547 0.06678324  0.06678324
 [9,] 1.00655058 0.04793098 2.74404860 0.31421420  0.31421420
[10,] 0.41427646 0.14302401 0.38961714 1.11569691  0.23892134
[11,] 0.02781791 0.02202251 0.03444122 0.02340237  0.03076160
[12,] 0.10432910 0.06706871 0.08259387 0.14296951  0.17056980
> 
> 
> 
> 
> dev.off()
null device 
          1 
>