Entering edit mode
Hello,
I've come across a problem in GRanges nearest, if subject of the
nearest call contains strand information (+/-) and the query does not
(*), the method takes a long time to run and raises warnings:
mm9.pro.gr and mm9.2ktiles.gr are both Granges objects.
> strandmm9.pro.gr) = "-"
> strandmm9.2ktiles.gr) = "*"
> system.time(nn <- nearestmm9.2ktiles.gr[1:5000],
mm9.pro.gr[1:5000]))
user system elapsed
27.150 0.002 27.416
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In start(ranges(x1Split[[st]])) - end(subSplit2) :
longer object length is not a multiple of shorter object length
2: In start(ranges(x1Split[[st]])) - end(subSplit2) :
longer object length is not a multiple of shorter object length
3: In start(ranges(x1Split[[st]])) - end(subSplit2) :
longer object length is not a multiple of shorter object length
4: In start(ranges(x1Split[[st]])) - end(subSplit2) :
longer object length is not a multiple of shorter object length
I think if a range in either query or subject is non-stranded (*)
both, the method should look for the nearest neighbor ignoring the
strand (at least that's my suggestion ;-).
If I set the strand info of the subject to "*" the method runs fine:
> strandmm9.pro.gr) = "*"
> system.time(nn <- nearestmm9.2ktiles.gr[1:5000],
mm9.pro.gr[1:5000]))
user system elapsed
0.264 0.000 0.264
If the query is "stranded" (+/-) and the subject isn't, the method
runs fine, too (though longer as if both query and subject are non-
stranded, but I guess this can be expected):
> system.time(nn <- nearestmm9.pro.gr[1:5000],
mm9.2ktiles.gr[1:5000], mm9.pro.gr[1:5000]))
user system elapsed
3.084 0.000 3.125
Another odd behavior is that if the query contains sequence names not
contained in the subject an error is raised the other way around
works fine. Wouldn't it make sense so set the vector elements of
sequences only found in the query to NA?
Kind regards,
Arne
[[alternative HTML version deleted]]
