CalculPWM: To calculate Position Weight Matrix

Description

This function calculates the PWM (Position Weigth Matrix) from set of aligned nucleotide sequences.

Usage

CalculPWM(matriu)

Arguments

Value

A matrix of characters

Author(s)

Erola Pairo <epeiroatibec.pcb.ub.es> and Joan Maynou <joan.maynouatupc.edu>

Examples

data(TranscriptionFactor)
matriu<-TranscriptionFactor
resul<-CalculPWM(matriu)

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/CalculPWM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CalculPWM
> ### Title: CalculPWM: To calculate Position Weight Matrix
> ### Aliases: CalculPWM
> 
> ### ** Examples
> 
> data(TranscriptionFactor)
> matriu<-TranscriptionFactor
> resul<-CalculPWM(matriu)
      [,1] [,2] [,3] [,4]
 [1,]    0    9    2    9
 [2,]    0   12    5    3
 [3,]    2    8    1    9
 [4,]   19    0    0    1
 [5,]    0    0    0   20
 [6,]    0    0    0   20
 [7,]    0    0   20    0
 [8,]    0    0    0   20
 [9,]    0    1    1   18
[10,]    2   10    2    6
[11,]    5    3    4    8
[12,]    4    5    6    5
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>