Christian,
I finished a round of changes to the subscript replacement operators in
IRanges, which will be available on bioconductor.org in BioC 2.5 after
the Wednesday builds have been pushed, and I should be able to meet your
needs. Just to be sure, can you provide a larger context what what
operation you are trying to perform? Some questions I have are:
1) What is the class and content of the replacement value?
2) How many columns in the RangedData values table are you looking to
replace?
3) What determines which rows within each of the spaces you are looking
to replace?
If you provide me with this information, I can let you know what the
most efficient way you can perform the replacement. Some example subset
replacement operations in place are:
values(x)[[i]][[j]] <- value # replace the jth column in the ith space
with value
values(x)[[i]][k,j] <- value # replace the (k,j) selection in the ith
space with value
values(x)[,j] <- value # replace columns denoted by j across all the
spaces with value
values(x)[i,j] <- value # using LogicalList, IntegerList, or RangesList
i, replace the selected rows within each of the spaces for columns
denoted by j with value
What I'm not sure of at this point is how flexible I should allow the
replacement value to be. Your feedback would be very helpful.
Cheers,
Patrick
Patrick Aboyoun wrote:
Christian,
Thanks for bringing this issue up. I have been meaning to improve the
subscript replacement functions in IRanges for some time and this
gives me a reason to make some improvements now. I need to put some
testing infrastructure in place to ensure the software is behaving as
expected, but the current solution I am working on for your problem
would look like
values(x)[[i]][[j]] <- value # set the jth column in the ith space
As this operation shows, I am working on the values table of the
RangedData object and not the whole object. This will complement the
current method of selecting the jth column in the ith space
values(x)[[i]][[j]] # get the jth column in the ith space
I'll let you know when this enhancement has been check-in.
Patrick
Christian Ruckert wrote:
I am missing a method to update only specific spaces of a RangedData
object.
Let 'x' be a 'RangedData' object.
The two existing methods are:
'x[i]': Subsets 'x' by indexing into its spaces, so the result is
of the same class, with a different set of spaces.
'x[[j]] <- value': Sets value as column 'j' in 'x', where 'j' can
be a character, numeric, or logical scalar that indexes into
the columns. The length of 'value' should equal 'nrow(x)'.
I am looking for a mixture of both, something like:
x[i][[j]] <- value
which actually doesn't work this way.
Any help would be appreciated,
Christian
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