edit some TODO comments

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@86948 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Mar 1, 2014 · 5630994 · 5630994
1 parent 622f7fb
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diff --git a/R/range-squeezers.R b/R/range-squeezers.R
@@ -13,7 +13,10 @@ setGeneric("grglist", signature="x",
 )
 
 ### Extract the ranges as a RangesList object.
-### TODO: This one should probably be in IRanges.
+### TODO: This one should probably be in IRanges together with ranges(), which
+### is another range-squeezer.
+### TODO: For consistency the ranges() generic should also get the 'use.mcols'
+### arg with default to FALSE.
 setGeneric("rglist", signature="x",
     function(x, use.mcols=FALSE, ...) standardGeneric("rglist")
 )

diff --git a/man/range-squeezers.Rd b/man/range-squeezers.Rd
@@ -68,9 +68,9 @@ rglist(x, use.mcols=FALSE, ...)
   \link[GenomicAlignments]{GAlignments}), the returned object is expected
   to be \emph{parallel} to \code{x}, that is, the i-th element in the output
   corresponds to the i-th element in the input. If \code{x} has names on it,
-  they're propagated to the returned object. If \code{use.mcols=TRUE} and
-  \code{x} has metadata columns on it, they're propagated to the returned
-  object.
+  they're propagated to the returned object. If \code{use.mcols} is TRUE and
+  \code{x} has metadata columns on it (accessible with \code{mcols(x)}),
+  they're propagated to the returned object.
 }
 
 \author{H. Pages}