Hi Charles, Vince, Herve,
A further option would be a DataFrame containing two GRanges columns. This
is used for example by the plyranges join_* and pair_* functions.
regards,
Paul Harrison
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Hi Charles, Vince,
Yes, a PairwiseAlignments object will contain the sequences of the 2
genomes being aligned so will be big. Could be mitigated by using one
object per chromosome instead of trying to represent the full genome
alignment in a single object, but then you loose the ability to
Starting from
PairwiseAlignments-class package:Biostrings R Documentation
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and
PairwiseAlignmentsSingleSubjectSummary objects
Description:
The ‘PairwiseAlignments’ class is a container for storing a set of
pairwise
Dear Bioc developers,
I am currently analysing pairwise genome alignments with Bioconductor,
and I represent them with a GRanges object of the first genome,
containing one element by alignment block, and storing the coordinates
in the other genome in a metadata column containing another
