[BioC] Sorting matrix by column
Axel Klenk
axel.klenk at actelion.com
Tue Oct 23 17:57:35 CEST 2012
Dear Manjula,
wow. How did you create that? :-)
order() doesn't like lists:
> order(list(1:3))
Error in order(list(1:3)) : unimplemented type 'list' in 'orderVector1'
and I think you should try to make your x look something like the
data.frame that Jim has used in his example and it will work.
Cheers,
Axel (not Alex!!) Klenk
Research Informatician
Information Management Drug Discovery
Actelion Pharmaceuticals Ltd. • Gewerbestrasse 16 • CH-4123 Allschwil
• Switzerland
G12.O1.R10
axel.klenk at actelion.com • www.actelion.com
Address for visitors: Hegenheimermattweg 92
On Tue, Oct 23, 2012 at 5:45 PM, Kasoji, Manjula (NIH/NCI) [C]
<manjula.kasoji at nih.gov> wrote:
> Hi Alex,
>
> Please see the output below:
>
>> str(x)
>
>
> List of 80
> $ : chr "10371400"
> $ : chr "10453900"
> $ : chr "10375051"
> $ : chr "10575211"
> $ : chr "10566254"
> $ : chr "10602372"
> $ : chr "10398428"
> $ : chr "10383518"
> $ : chr "10397054"
> $ : chr "10384020"
> $ : chr "10608710"
> $ : chr "10363762"
> $ : chr "10375058"
> $ : chr "10381603"
> $ : chr "10442373"
> $ : chr "10421227"
> $ : chr "10534966"
> $ : chr "10398408"
> $ : chr "10398418"
> $ : chr "10572772"
> $ : chr "Lypla1"
> $ : chr "Tcea1"
> $ : chr "Atp6v1h"
> $ : chr "Oprk1"
>
>> class(x[,2])
> [1] "list"
>
>
>
>
> On 10/23/12 11:42AM, "Axel Klenk" <axel.klenk at actelion.com> wrote:
>
>>Dear Guest,
>>
>>I think your approach is valid in general and it is your x that is
>>causing the
>>problem; column 'Gene Symbol' appears to contain two values. What is the
>>result of
>>
>>str(x)
>>
>>and/or
>>
>>class(x[,2])
>>
>>?
>>
>>Cheers,
>>
>> - axel
>>
>>
>>Axel Klenk
>>Research Informatician
>>Information Management Drug Discovery
>>
>>Actelion Pharmaceuticals Ltd. € Gewerbestrasse 16 € CH-4123 Allschwil
>>€ Switzerland
>>G12.O1.R10
>>
>>axel.klenk at actelion.com € www.actelion.com
>>Address for visitors: Hegenheimermattweg 92
>>
>>
>>
>>On Tue, Oct 23, 2012 at 5:15 PM, Guest [guest] <guest at bioconductor.org>
>>wrote:
>>>
>>>
>>> Hi,
>>>
>>> I would like to sort a matrix by a specific column (column 2). I tried
>>>the order() function, but I get an error. I think it is because the
>>>values in column 2 are not numeric, they are gene symbols. This may be a
>>>general R question, but I thought I would post it here since it is
>>>microarray data analysis.
>>>
>>> I have matrix x:
>>>
>>> > x
>>> ID Gene Symbol logFC Adj.PVal
>>> 10344624 "10371400" "Lypla1" 0.3592492 0.9999522
>>> 10344633 "10453900" "Tcea1" 0.1886117 0.9999522
>>> 10344637 "10375051" "Atp6v1h" 0.6713107 0.9999522
>>> 10344653 "10575211" "Oprk1" -0.2342731 0.9999522
>>> 10344658 "10566254" "Rb1cc1" 1.790676 0.9999522
>>> 10344674 "10602372" "Fam150a" 1.397496 0.9999522
>>> 10344679 "10398428" "St18" -0.3278807 0.9999522
>>> 10344707 "10383518" "Pcmtd1" -0.2231074 0.9999522
>>> 10344713 "10397054" "Ahcy" -0.1844897 0.9999522
>>> 10344723 "10384020" "Rrs1" -0.2322781 0.9999522
>>> 10344725 "10608710" "Adhfe1" 0.5993566 0.9999522
>>> 10344741 "10363762" "Hnrnpa3" -0.2660978 0.9999522
>>> 10344743 "10375058" "3110035E14Rik" 0.9178868 0.9999522
>>> 10344750 "10381603" "Sgk3" -0.2961638 0.9999522
>>> 10344772 "10442373" "6030422M02Rik" -0.1653454 0.9999522
>>> 10344789 "10421227" "Cspp1" -0.1480766 0.9999522
>>> 10344799 "10534966" "Cspp1" -0.2436361 0.9999522
>>> 10344801 "10398408" "Cspp1" -0.4040665 0.9999522
>>> 10344803 "10398418" "Cspp1" -0.2556627 0.9999522
>>> 10344805 "10572772" "Cspp1" -0.1864641 0.9999522
>>>
>>> I want to sort on the "Gene Symbol" column so that I can remove the
>>>duplicates and keep the one with the highest log fold change.
>>>
>>> I tried the following and received an error.
>>> > x[order(x[,2]),]
>>> Error in order(x[, 2]) : unimplemented type 'list' in 'orderVector1'
>>>
>>> If anyone has any suggestions for an easy way to sort a significant
>>>gene list, remove duplicated values, and keep the value with highest
>>>fold change, that would be helpful!
>>>
>>> I've posted my session info below.
>>>
>>> Thanks!
>>>
>>> Guest
>>>
>>> -- output of sessionInfo():
>>>
>>> > sessionInfo()
>>> R version 2.15.1 (2012-06-22)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.15.1
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>
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>
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