[BioC] Sorting matrix by column

Tue Oct 23 17:38:05 CEST 2012

Hi Jim,

The R session info below does correspond to the session I pasted. When I
tried your suggestion, I still get an error:

> x[base::order(x[,2]),]
Error in base::order(x[, 2]) :
  unimplemented type 'list' in 'orderVector1'

I see that you don't have quotes around the ID and Gene Symbol names in
your matrix. Is there a way to remove the quotes?

Thanks!

On 10/23/12 11:27AM, "James W. MacDonald" <jmacdon at uw.edu> wrote:

>
>
>On 10/23/2012 11:15 AM, Guest [guest] 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'
>
>I am not sure the sessionInfo() you give below corresponds to the
>session above. I get:
>
> > x <- data.frame(ID = 12345:12354, Gene =
>Rkeys(mogene10sttranscriptclusterSYMBOL)[5001:5010], logFC = rnorm(10),
>pval = runif(10))
> > x
>       ID   Gene       logFC      pval
>1  12345  Sepw1  0.56914952 0.4916910
>2  12346  Serf1  0.83929962 0.4816986
>3  12347 Gm4748  0.12462117 0.9372249
>4  12348   Sez6 -0.21468480 0.4921201
>5  12349  Foxp3 -1.36283694 0.4575675
>6  12350  Sfpi1  1.03632565 0.5251826
>7  12351  Sfrp1  0.04689108 0.3068112
>8  12352   Frzb  0.08379607 0.1509499
>9  12353  Sfrp4 -1.61513620 0.9336235
>10 12354  Srsf2  1.56222316 0.2571122
> > x[order(x[,2]),]
>       ID   Gene       logFC      pval
>5  12349  Foxp3 -1.36283694 0.4575675
>8  12352   Frzb  0.08379607 0.1509499
>3  12347 Gm4748  0.12462117 0.9372249
>1  12345  Sepw1  0.56914952 0.4916910
>2  12346  Serf1  0.83929962 0.4816986
>4  12348   Sez6 -0.21468480 0.4921201
>6  12350  Sfpi1  1.03632565 0.5251826
>7  12351  Sfrp1  0.04689108 0.3068112
>9  12353  Sfrp4 -1.61513620 0.9336235
>10 12354  Srsf2  1.56222316 0.2571122
>
>It appears you have something loaded that thinks you want to use the
>orderVector1() function. You can always specify the function you are
>intending with the :: operator (in this case, you want base::order()).
>
> > x[base::order(x[,2]),]
>       ID   Gene       logFC      pval
>5  12349  Foxp3 -1.36283694 0.4575675
>8  12352   Frzb  0.08379607 0.1509499
>3  12347 Gm4748  0.12462117 0.9372249
>1  12345  Sepw1  0.56914952 0.4916910
>2  12346  Serf1  0.83929962 0.4816986
>4  12348   Sez6 -0.21468480 0.4921201
>6  12350  Sfpi1  1.03632565 0.5251826
>7  12351  Sfrp1  0.04689108 0.3068112
>9  12353  Sfrp4 -1.61513620 0.9336235
>10 12354  Srsf2  1.56222316 0.2571122
>
>Best,
>
>Jim
>
>
>>
>> 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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>
>-- 
>James W. MacDonald, M.S.
>Biostatistician
>University of Washington
>Environmental and Occupational Health Sciences
>4225 Roosevelt Way NE, # 100
>Seattle WA 98105-6099
>