To line up Transcription Factor Binding sites through Multiple Sequence Alignment (MSA)

Description

This function, Alignment, lines up Transcription Factor Binding Sites, TFBS, through MSA. There are different kinds of MSA: MEME, Clustalw and Muscle

Usage

Alignment(TF,iicc)

Arguments

Author(s)

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

Examples

require("MEET")
data(iicc)
pathMEET <- system.file("sequences", package = "MEET")
Alignment(TF=paste(pathMEET, "AP1.fa", sep = "/"),iicc)

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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> 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/Alignment.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Alignment
> ### Title: To line up Transcription Factor Binding sites through Multiple
> ###   Sequence Alignment (MSA)
> ### Aliases: Alignment
> 
> ### ** Examples
> 
> require("MEET")
> data(iicc)
> pathMEET <- system.file("sequences", package = "MEET")
> Alignment(TF=paste(pathMEET, "AP1.fa", sep = "/"),iicc)
      [,1] [,2] [,3] [,4] [,5] [,6] [,7]
 [1,] "T"  "G"  "A"  "C"  "T"  "C"  "A" 
 [2,] "T"  "G"  "A"  "G"  "T"  "C"  "A" 
 [3,] "T"  "G"  "A"  "G"  "T"  "C"  "A" 
 [4,] "T"  "G"  "A"  "G"  "T"  "C"  "A" 
 [5,] "T"  "G"  "A"  "G"  "T"  "C"  "A" 
 [6,] "T"  "G"  "A"  "A"  "T"  "C"  "A" 
 [7,] "T"  "G"  "A"  "A"  "T"  "C"  "A" 
 [8,] "A"  "G"  "T"  "G"  "T"  "C"  "A" 
 [9,] "T"  "G"  "A"  "G"  "T"  "C"  "A" 
[10,] "T"  "G"  "A"  "G"  "T"  "A"  "A" 
[11,] "T"  "G"  "A"  "T"  "T"  "C"  "A" 
[12,] "T"  "C"  "A"  "G"  "T"  "C"  "A" 
[13,] "T"  "G"  "C"  "G"  "T"  "C"  "A" 
[14,] "T"  "G"  "A"  "G"  "T"  "C"  "A" 
[15,] "T"  "G"  "A"  "C"  "G"  "C"  "G" 
[16,] "T"  "G"  "A"  "T"  "T"  "A"  "A" 
[17,] "T"  "T"  "C"  "C"  "T"  "G"  "G" 
[18,] "T"  "C"  "T"  "T"  "T"  "C"  "A" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>