Open balwierz opened 5 years ago
I agree with @balwierz, I don't see a problem with #141 and after removing mentioned by @balwierz function (https://github.com/BIMSBbioinfo/genomation/blob/master/R/Ops.R#L112) everything works well. @al2na @frenkiboy are u ok with removing:
setMethod("[",signature(x="ScoreMatrixList", i = "ANY"),
function(x,i){
tmp=sml@.Data[i]
names(tmp)=names(x)[i]
ScoreMatrixList( tmp)
}
)
?
underlying issue might have been fixed with newer R versions, if it doesn't break anything downstream I'm ok with removing. It looks like it shouldn't but maybe we run check first ?
check on it looks as before, no errors, no warnings if there are no arguments to keep it, then I'll remove it (@frenkiboy, if it would cause any problems in your code, I'll recheck it and try to make it work for everyone)
Thanks. I have also removed the "names" slot in ScoreMatrixList definition as it was introduced in the fix of #141
I just reverted the commit that supposed to fix this issue until a better solution will be found, because it fails BioC check.
The hack introduced in https://github.com/BIMSBbioinfo/genomation/issues/141 breaks the possibility of subsetting elements of ScoreMatrixList by names.
If I undo that commit i.e. remove names slot from ScoreMatrixList class and delete the following function:
from Ops.R I unbreak the correct behaviour.
Not only this. I don't see the original problem mentioned in #141 at all. Subsetting a ScoreMatrixList preserves names.