Position Specific Scoring Matrices from a set of aligned sequences

Description

Calculate a PSSM of a set of DNA aligned sequences, taking into account background probabilities. The output is the logodds matrix.

Usage

CalculPSSM(matriu, Prob)

Arguments

Value

logodds: logodds matrix calculated as a log2 of the frequency matrix

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

CalculInformation

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/CalculPSSM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CalculPSSM
> ### Title: Position Specific Scoring Matrices from a set of aligned
> ###   sequences
> ### Aliases: CalculPSSM
> 
> ### ** Examples
> 
> data(TranscriptionFactor)
> data(BackgroundOrganism)
> CalculPSSM(matriu=TranscriptionFactor, Prob=Prob)
            [,1]        [,2]       [,3]       [,4]
 [1,] -4.3923174  0.47186872  1.2801079 -0.7940581
 [2,] -4.3923174 -1.01727799  1.6880560  0.4545659
 [3,] -1.5343364  0.47186872  1.1137146 -1.6795994
 [4,]  1.5235620 -2.34792330 -4.3923174 -4.3923174
 [5,] -4.3923174  1.59636726 -4.3923174 -4.3923174
 [6,] -4.3923174  1.59636726 -4.3923174 -4.3923174
 [7,] -4.3923174 -4.39231742 -4.3923174  2.4164680
 [8,] -4.3923174  1.59636726 -4.3923174 -4.3923174
 [9,] -4.3923174  1.44688637 -1.6795994 -1.6795994
[10,] -1.5343364 -0.08853667  1.4292794 -0.7940581
[11,] -0.3370350  0.30812230 -0.2493595  0.1451167
[12,] -0.6374299 -0.33703499  0.4545659  0.7092206
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>