Jonathan Carroll jonocarroll

Combining SummarizedExperiment objects

Peter Hickey
20 October 2015

Motivation

I often find myself with multiple SE objects (I'm using SE as a shorthand for the SummarizedExperiment0 and RangedSummarizedExeriment classes), each with potentially non-distinct samples and potentially non-overlapping features/ranges. Currently, it is difficult to combine these objects; rbind() can only combine objects with the same samples but distinct features/ranges and cbind() can only combine objects with the same features/ranges but distinct samples. I think it would be useful to have a "combine" method for SE objects that handles the most general situation where each object has potentially non-distinct samples and potentially non-overlapping features/ranges.

People

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😏 `:smirk:`	😍 `:heart_eyes:`	😘 `:kissing_heart:`
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	%%-----------------------------------------------------------------------
	%% Make your own quadrille, graph, hex, etc paper!
	%% Uses the pgf/TikZ package for LaTeX, which should be part of
	%% any modern TeX installation.
	%% Email: [email protected]
	%% Twitter: @mcnees
	%%-----------------------------------------------------------------------

	\documentclass[11pt]{article}

	variables:
	CODECOV_TOKEN: "CODECOV_TOKEN_STRING"
	_R_CHECK_CRAN_INCOMING_: "false"
	_R_CHECK_FORCE_SUGGESTS_: "true"
	APT_PKGS: "libcurl4-openssl-dev libssh2-1-dev libssl-dev libxml2-dev zlib1g-dev git"

	before_script:
	- apt-get update
	- apt-get install -y --no-install-recommends ${APT_PKGS}
	- apt-get install -y --no-install-recommends qpdf pandoc pandoc-citeproc

	private static readonly string[] tenHoursOfFun =
	{
	"https://www.youtube.com/watch?v=wbby9coDRCk",
	"https://www.youtube.com/watch?v=nb2evY0kmpQ",
	"https://www.youtube.com/watch?v=eh7lp9umG2I",
	"https://www.youtube.com/watch?v=z9Uz1icjwrM",
	"https://www.youtube.com/watch?v=Sagg08DrO5U",
	"https://www.youtube.com/watch?v=5XmjJvJTyx0",
	"https://www.youtube.com/watch?v=IkdmOVejUlI",
	"https://www.youtube.com/watch?v=jScuYd3_xdQ",

	## 2015-11-11 NOTE!
	## with_libpaths() is one of the functions removed (well, deprecated, for now) from
	## devtools
	## it's in withr now!
	## see newer script below!!!

	library(devtools) # with_lib(), install_github()

	tmp_lib <- "~/tmp/tmp_lib"
	dir.create(tmp_lib)

	---
	title: "twee demo"
	author: "Jenny Bryan"
	date: "17 August, 2014"
	output:
	html_document:
	toc: TRUE
	keep_md: TRUE
	---