[Bioc-devel] coerce ExpressionSet to SummarizedExperiment
Levi Waldron
lwaldron.research at gmail.com
Mon Sep 11 16:15:56 CEST 2017
Thanks Martin! I see the RangedSummarizedExperiment coercion method works
when there are no mappable ranges (for example curatedMetagenomicData
ExpressionSet objects), although the rowRanges is a GRangesList of empty
elements. It might be worth also having a SummarizedExperiment coercion
method it it's not a problematic or big job. And now I suppose I can ask
the question I *really* wanted to know, which is why can't I coerce an
object that extends eSet? I can still use the SummarizedExperiment()
constructor, but for example:
> library(metagenomeSeq)> data(mouseData)> class(mouseData)[1] "MRexperiment"
attr(,"package")
[1] "metagenomeSeq"> is(mouseData, "ExpressionSet")[1] FALSE>
is(mouseData, "eSet")[1] TRUE
> SummarizedExperiment(mouseData)class: SummarizedExperiment
dim: 10172 139
metadata(0):
assays(1): ''
rownames(10172): Prevotellaceae:1 Lachnospiraceae:1 ... Bryantella:103
Parabacteroides:956
rowData names(0):
colnames(139): PM1:20080107 PM1:20080108 ... PM9:20080225 PM9:20080303
colData names(0):
> as(mouseData, "RangedSummarizedExperiment") Error in as(mouseData,
"RangedSummarizedExperiment") : no method or default for coercing
“MRexperiment” to “RangedSummarizedExperiment” > as(mouseData,
"SummarizedExperiment") Error in as(mouseData, "SummarizedExperiment") : no
method or default for coercing “MRexperiment” to
“SummarizedExperiment” > as(mouseData,
"ExpressionSet") Error in updateOldESet(from, "ExpressionSet") : no slot of
name "pData" for this object of class "AnnotatedDataFrame" >
On Mon, Sep 11, 2017 at 6:58 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
> On 09/10/2017 08:38 PM, Levi Waldron wrote:
>
>> I just dug up this old thread because I realized we still don't have a
>> coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we
>>
>
> try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see
> ?makeSummarizedExperimentFromExpressionSet
>
> do have SummarizedExperiment(sample.ExpressionSet), could the coercion
>> method also be added easily?
>>
>> library(Biobase) > library(SummarizedExperiment) >
>>>
>> example("ExpressionSet")
>>
>> SummarizedExperiment(sample.ExpressionSet)class: SummarizedExperiment
>>>
>> dim: 500 26
>> metadata(0):
>> assays(1): ''
>> rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
>> rowData names(0):
>> colnames(26): A B ... Y Z
>> colData names(0):> as(sample.ExpressionSet,
>> "SummarizedExperiment")Error in as(sample.ExpressionSet,
>> "SummarizedExperiment") :
>> no method or default for coercing “ExpressionSet” to
>> “SummarizedExperiment”
>>
>> sessionInfo()R version 3.4.0 RC (2017-04-20 r72569)
>>>
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.3 LTS
>>
>> Matrix products: default
>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> LC_TIME=en_US.UTF-8
>> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
>> LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4 parallel stats graphics grDevices utils
>> datasets methods base
>>
>> other attached packages:
>> [1] SummarizedExperiment_1.7.5 DelayedArray_0.3.16
>> matrixStats_0.52.2
>> [4] GenomicRanges_1.29.6 GenomeInfoDb_1.13.4
>> IRanges_2.11.7
>> [7] S4Vectors_0.15.5 Biobase_2.37.2
>> BiocGenerics_0.23.0
>>
>> loaded via a namespace (and not attached):
>> [1] lattice_0.20-35 bitops_1.0-6 grid_3.4.0
>> [4] zlibbioc_1.23.0 XVector_0.17.0 Matrix_1.2-11
>> [7] tools_3.4.0 RCurl_1.95-4.8 compiler_3.4.0
>> [10] GenomeInfoDbData_0.99.1
>>
>>
>>>
>> On Mon, Sep 22, 2014 at 1:54 AM, Hervé Pagès <hpages at fhcrc.org> wrote:
>>
>> Hi,
>>>
>>> On 09/20/2014 11:14 AM, Martin Morgan wrote:
>>>
>>> On 09/20/2014 10:43 AM, Sean Davis wrote:
>>>>
>>>> Hi, Vince.
>>>>>
>>>>> Looks like a good start. I'd probably pull all the assays from
>>>>> ExpressionSet into SummarizedExperiment as the default, avoiding data
>>>>> coercion methods that are unnecessarily lossy. Also, as it stands, the
>>>>> assayname argument is not used anyway?
>>>>>
>>>>>
>>>> I think there will be some resistance to uniting the 'Biobase' and
>>>> 'IRanges' realms under 'GenomicRanges';
>>>>
>>>>
>>> This coercion method could be defined (1) in Biobase (where
>>> ExpressionSet is defined), (2) in GenomicRanges (where
>>> SummarizedExperiment is defined), or (3) in a package that
>>> depends on Biobase and GenomicRanges.
>>>
>>> Since it's probably undesirable to make Biobase depend on GenomicRanges
>>> or vice-versa, we would need to use Suggests for (1) or (2). That
>>> means we would get a note like this at installation time:
>>>
>>> ** preparing package for lazy loading
>>> in method for ‘coerce’ with signature ‘"ExpressionSet","SummarizedEx
>>> periment"’:
>>> no definition for class “SummarizedExperiment”
>>>
>>> Not very clean but it works.
>>>
>>> (3) is a cleaner solution but then the coercion method would
>>> not necessarily be available to the user when s/he needs it (unless
>>> s/he knows what extra package to load). The obvious advantage of
>>> putting the method in Biobase is that if a user has an ExpressionSet,
>>> then s/he necessarily has Biobase attached and the method is already
>>> in her/his search path.
>>>
>>> Another solution would be (4) to move SummarizedExperiment somewhere
>>> else. That would be in a package that depends on GenomicRanges and
>>> Biobase, and the coercion method would be defined there.
>>>
>>> H.
>>>
>>>
>>> considerable effort has gone in
>>>
>>>> to making a rational hierarchy of package dependencies [perhaps Herve
>>>> will point to some of his ASCII art on the subject].
>>>>
>>>> I have some recollection of (recent) discussion related to this topic in
>>>> the DESeq2 realm, but am drawing a blank; presumably Michael or Wolfgang
>>>> or ... will chime in.
>>>>
>>>> Martin
>>>>
>>>>
>>>> Sean
>>>>>
>>>>>
>>>>> On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey
>>>>> <stvjc at channing.harvard.edu>
>>>>> wrote:
>>>>>
>>>>> do we have a facility for this?
>>>>>
>>>>>>
>>>>>> if not, we have
>>>>>>
>>>>>> https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R
>>>>>>
>>>>>> https://github.com/vjcitn/biocMultiAssay/blob/master/man/coe
>>>>>> rce-methods.Rd
>>>>>>
>>>>>>
>>>>>> it occurred to me that we might want something like this in
>>>>>> GenomicRanges
>>>>>> (that's where SummarizedExperiment is managed, right?) and I will add
>>>>>> it
>>>>>> if there are no objections
>>>>>>
>>>>>> the arguments are currently
>>>>>>
>>>>>> assayname = "exprs", # for naming SimpleList element
>>>>>> fngetter =
>>>>>> function(z) rownames(exprs(z)), # extract usable
>>>>>> feature names
>>>>>> annDbGetter =
>>>>>> function(z) {
>>>>>> clnanno = sub(".db", "", annotation(z))
>>>>>> stopifnot(require(paste0(annotation(z), ".db"),
>>>>>> character.only=TRUE) )
>>>>>> get(paste0(annotation(z), ".db")) # obtain resource
>>>>>> for
>>>>>> mapping feature names to coordinates
>>>>>> },
>>>>>> probekeytype = "PROBEID", # chipDb field to use
>>>>>> duphandler = function(z) { # action to take to process
>>>>>> duplicated
>>>>>> features
>>>>>> if (any(isd <- duplicated(z[,"PROBEID"])))
>>>>>> return(z[!isd,,drop=FALSE])
>>>>>> z
>>>>>> },
>>>>>> signIsStrand = TRUE, # verify that signs of addresses define
>>>>>> strand
>>>>>> ucsdChrnames = TRUE # prefix 'chr' to chromosome token
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fhcrc.org
>>> Phone: (206) 667-5791
>>> Fax: (206) 667-1319
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>>
>>
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--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 Skype:
levi.waldron
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