MsaMetaData-class: Class 'MsaMetaData'

In msa: Multiple Sequence Alignment

Description

S4 class for storing metadata about multiple sequence alignment results

Objects

Objects of this virtual class are not be created and used directly. This is an auxiliary class used by the classes MsaAAMultipleAlignment, MsaDNAMultipleAlignment, and MsaRNAMultipleAlignment

Slots

The following slots are defined for MsaMetaData objects:

version:

slot in which information is stored with which algorithm the multiple alignment has been computed along with its version number.

params:

list in which the parameters are stored with which the multiple alignment algorithm has been executed.

call:

the matched call with which the object was created

Methods

version(object):

accessor to the version slot

params(x):

accessor to the params slot

Author(s)

Enrico Bonatesta and Christoph Horejs-Kainrath <[e-mail]>

References

http://www.bioinf.jku.at/software/msa

U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.

See Also

msa, msaClustalW, msaClustalOmega, msaMuscle, MsaAAMultipleAlignment, MsaDNAMultipleAlignment, MsaRNAMultipleAlignment

Examples

## read sequences
filepath <- system.file("examples", "exampleAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)

## simple call with default values
myAlignment <- msaClustalOmega(mySeqs)

## show the algorithm version with which the results were created
version(myAlignment)

## show the results
show(myAlignment)

## print the results
print(myAlignment, show="alignment")
print(myAlignment, show=c("alignment", "version"))
print(myAlignment, show="standardParams")
print(myAlignment, show="algParams")
print(myAlignment, show=c("call", "version"))

## show the params
params(myAlignment)

Example output

Loading required package: Biostrings
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

using Gonnet
[1] "ClustalOmega 1.2.0"
ClustalOmega 1.2.0 

Call:
   msaClustalOmega(mySeqs)

MsaAAMultipleAlignment with 9 rows and 467 columns
    aln                                                    names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus 

MsaAAMultipleAlignment with 9 rows and 467 columns
    aln                                                    names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus 
ClustalOmega 1.2.0 

MsaAAMultipleAlignment with 9 rows and 467 columns
    aln                                                    names
[1] MSALVLESRALGRKLSDFGQETSYIE...LKI-LADSISSEVEILCSALQKLK- PH4H_Bos_taurus
[2] MSTAVLENPGLGRKLSDFGQETSYIE...LKI-LADSINSEIGILCSALQKIK- PH4H_Homo_sapiens
[3] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCNALQKIKS PH4H_Rattus_norve...
[4] MAAVVLENGVLSRKLSDFGQETSYIE...LKI-LADSINSEVGILCHALQKIKS PH4H_Mus_musculus
[5] --------------------------...------------------------- PH4H_Pseudomonas_...
[6] --------------------------...------------------------- PH4H_Rhizobium_loti
[7] --------------------------...YATAGGRLAGAAAG----------- PH4H_Caulobacter_...
[8] --------------------------...GWADTEDV----------------- PH4H_Chromobacter...
[9] --------------------------...GWADTADI----------------- PH4H_Ralstonia_so...
Con --------------------------...???-?AD???????----------- Consensus 
Standard params:
   gapOpening = default
   gapExtension = default
   maxiters = 0
   verbose = FALSE
Options specific to ClustalOmega 1.2.0:
   inputSeqIsFileFlag = FALSE
   outputOrder = tree-order
   auto = FALSE
   dealign = FALSE
   force = FALSE
   full = FALSE
   fullIter = FALSE
   isProfile = FALSE
   longVersion = FALSE
   percentId = FALSE
   residueNumber = FALSE
   useKimura = FALSE
   version = FALSE
ClustalOmega 1.2.0 

Call:
   msaClustalOmega(mySeqs)
$gapOpening
[1] "default"

$gapExtension
[1] "default"

$maxiters
[1] 0

$verbose
[1] FALSE

$inputSeqIsFileFlag
[1] FALSE

$outputOrder
[1] "tree-order"

$auto
[1] FALSE

$dealign
[1] FALSE

$force
[1] FALSE

$full
[1] FALSE

$fullIter
[1] FALSE

$isProfile
[1] FALSE

$longVersion
[1] FALSE

$percentId
[1] FALSE

$residueNumber
[1] FALSE

$useKimura
[1] FALSE

$version
[1] FALSE

msa documentation built on Nov. 8, 2020, 5:41 p.m.