Conversion from CNEr::Axt objects
Note
By default, in the Axt objects produced by the CNEr::readAxt
function, the coordinates of the query genome are represented with the same
numerical value as in the original file. In Axt files, when the alignment
is on the minus strand, the query genome coordinates have their origin on
the reverse-complement strand. Therefore, although in the CNEr object
they are stored in a GRanges object, they do not represent genomic ranges.
In order to do so, there is a CNEr::fixCoordinates function.
See also
Other Bioconductor API functions:
GBreaks-class,
getSeq(),
pairwiseAlignment(),
range_GBreaks(),
reverse(),
subsetByOverlaps_GBreaks()