Question: msa: How to obtain a subset of an alignment
gravatar for Christof Winter
23 months ago by
TU München
Christof Winter10 wrote:

I am using the msa package to align DNA sequences with Muscle (which works great!). Now I was wondering whether it's possible to extract a subset of an alignment. In the following example, I would like to extract just the first 3 rows from the alignment:


mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa")
mySequences <- readAAStringSet(mySequenceFile)

aln <- msa(mySequences)

# subset, get first 3 only
rowmask(aln, invert=TRUE) <- IRanges(start=1, end=3)

print(aln, show="complete")

However, the masked rows are still present and are showing up with # characters. How can I drop the masked parts in order to have just the first 3 rows in an alignment object? 

ADD COMMENTlink modified 23 months ago by UBodenhofer250 • written 23 months ago by Christof Winter10
Answer: msa: How to obtain a subset of an alignment
gravatar for UBodenhofer
23 months ago by
Johannes Kepler University, Linz, Austria
UBodenhofer250 wrote:

Thanks for your positive feedback, Christof! 

Regarding your question: yes, it is true that objects of class 'MultipleAlignment' and classes derived from 'MultipleAlignment' do not support subsetting. Presently, I can offer the following workaround (... continuing your example code):

alnSubset <- as(AAMultipleAlignment(unmasked(aln)[1:3]),

print(alnSubset, show="complete")

I admit that this is not very elegant. Moreover, all metadata describing the alignment is lost. I am actually considering adding some more casts to the package or maybe even subsetting methods. Maybe somebody else has some thoughts on this subject?

ADD COMMENTlink written 23 months ago by UBodenhofer250

Please, please add some subsetting methods. You have the easiest and most flexible of the BioConductor alignment systems. Just needs the ability to get inside to do analyses we need to do, not just the standard ones. Thanks.

ADD REPLYlink written 9 months ago by jameshunterbr0
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