From 563099416d0674454c86a3df0387c9b10a08a0f3 Mon Sep 17 00:00:00 2001 From: "hpages@fhcrc.org" Date: Sat, 1 Mar 2014 00:40:14 +0000 Subject: [PATCH] edit some TODO comments git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@86948 bc3139a8-67e5-0310-9ffc-ced21a209358 --- R/range-squeezers.R | 5 ++++- man/range-squeezers.Rd | 6 +++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/R/range-squeezers.R b/R/range-squeezers.R index 8ba1bdc..facf666 100644 --- 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 index 0c79417..d196d64 100644 --- 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}