03-align: Class '"AlignedCluster"'

In SVAlignR: Recovering Structure of Long Molecules from Structural Variation Data

Class "AlignedCluster"

Description

The AlignedCluster class is used to align a set of clustered sequences. The alignClusters function creates a new object of the AlignedCluster class. The alignAllClusters function takes a SequenceCluster object and returns a list of AlignedCluster objects. Clustering is performed using the ClustalW algorithm. The associated class and functions take care of encoding and decoding sequences into a form that can be used by the implementation of ClustalW in the msa package.

Usage

alignCluster(sequences, mysub = NULL, gapO = 10, gapE = 0.2)
alignAllClusters(sc, mysub = NULL, gapO = 10, gapE = 0.2)
makeSubsMatrix(match = 5, mismatch = -2)
## S4 method for signature 'AlignedCluster'
image(x, col = "black", cex = 1, main = "", ...)

Arguments

sequences	A character vector that contains all sequences to be aligned.
mysub	A square (usually symmetric) substitution matrix.
gapO	A numeric value defining the penalty for opening a gap.
gapE	A numeric value defining the penalty for extending a gap.
sc	An object of the SequenceCluster class.
match	A numeric value defining the reward for matching symbols from two sequences.
mismatch	A numeric value defining the penalty for mismatching symbols from two sequences.
x	An object of the AlignedCluster class.
col	A character setting the color of annotations in the image.
main	Character; the plot title.
cex	Numeric; size of teh text inside the image of the alignment matrix.
...	Extra arguments for generic or plotting routines.

Value

The alignCluster function returns a new object of the AlignedCluster class. The alignAllClusters function returns a list of AlignedCluster objects. The makeSubMatrix function returns a symmetric substitution matrix.

Objects from the Class

Objects should be defined using the alignCluster or alignAllCluster functions. You typically pass in a character vector of sequences that have already been found to form a cluster.

Slots

alignment:

A matrix of aligned sequences; rows are sequences and columns are aligned positions..

weights

A numeric vactor; the numbof times each unique raw sequence occurs.

consensus:

A character vector; the consensus sequence of a successful alignment.

Details

Alignment is performed using the implementation of the ClustalW algorithm provided by the msa package. The existing code to align amino-acid protein sequences is used by converting the current alphabet to one that limits its use to the known amino acids. The decision to ue this method introduces a limitation: we are unable to align any set of seqeunces that use more than 25 distinct symbols. Attempting such an alignment will result in the alignCluster function returning a NULL value, which is passed on as one of the list items from alignAllClusters.

Note

These functions will only work if the ms package is installed. At the time of writing, CRAN does not install msa because of the way that msa uses the OpenMP protocol. So, SVAlignR only "Suggests" using the package and does not include it in the list of "Imports". Thus, to obtain this functionality, you must manually install msa from the yourself using the BiocManager::install function from BioConductor.

Author(s)

Kevin R. Coombes <[e-mail]>

Examples

data(longreads)
seqs <- longreads$connection[1:15]
pad <- c(rep("0", 9), rep("", 6))
names(seqs) <- paste("LR", pad, 1:length(seqs), sep = "")
seqs <- seqs[!duplicated(seqs)]
mysub <- makeSubsMatrix(match = 2, mismatch = -6)
if (!requireNamespace("msa", quietly = TRUE)) {
  warning("Cluster alignment is only available if the 'msa' package is installed.\n")
} else {
  ab <- alignCluster(seqs, mysub)
  image(ab)
}

SVAlignR documentation built on Sept. 20, 2025, 3:01 p.m.