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Question: incorrect biomaRt output order of gene list
0
gravatar for Yuqia
8 months ago by
Yuqia0
Switzerland
Yuqia0 wrote:

Hello,

I have another problem with biomaRt.

My ranked list of differentially expressed genes (ENSG...) are not ordered by the id number but by the expression fold change (naturally):

> library(biomaRt)
> mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
> list <- as.vector(testBiomaRt)
> list

                V1
1  ENSG00000185247
2  ENSG00000268089
3  ENSG00000151136
4  ENSG00000054793
5  ENSG00000121895
6  ENSG00000172264
7  ENSG00000162409
8  ENSG00000142698
9  ENSG00000132109
10 ENSG00000140090

But after I used getBM function to get the gene names for the list:

> res <- getBM(attributes = c('ensembl_gene_id', 'external_gene_name'),                     
             filters = 'ensembl_gene_id', 
             values = list,
             mart = mart)

> res

the result is a list shuffled by the ranked ENSG number from lowest to highest:

ensembl_gene_id                external_gene_name
1  ENSG00000054793              ATP9A
2  ENSG00000121895            TMEM156
3  ENSG00000132109             TRIM21
4  ENSG00000140090            SLC24A4
5  ENSG00000142698            C1orf94
6  ENSG00000151136             BTBD11
7  ENSG00000162409             PRKAA2
8  ENSG00000172264            MACROD2
9  ENSG00000185247            MAGEA11
10 ENSG00000268089              GABRQ

How can I maintain the original rank order of my input list in the output?

Thank you!

ADD COMMENTlink modified 8 months ago • written 8 months ago by Yuqia0
0
gravatar for James W. MacDonald
8 months ago by
United States
James W. MacDonald48k wrote:

You shouldn't expect results from biomaRt to be sorted in any particular way, since it's at heart a database query and those come back unsorted. Instead you should query on the filter as well (like you did in the second example) and then use match to re-order correctly.

> library(org.Hs.eg.db)
> ensgs <- head(keys(org.Hs.eg.db, "ENSEMBL"), 30)
> ensgs
 [1] "ENSG00000121410" "ENSG00000175899" "ENSG00000256069" "ENSG00000171428"
 [5] "ENSG00000156006" "ENSG00000196136" "ENSG00000114771" "ENSG00000127837"
 [9] "ENSG00000129673" "ENSG00000090861" "ENSG00000183044" "ENSG00000165029"
[13] "ENSG00000107331" "ENSG00000167972" "ENSG00000131269" "ENSG00000204574"
[17] "ENSG00000225989" "ENSG00000232169" "ENSG00000206490" "ENSG00000236149"
[21] "ENSG00000236342" "ENSG00000231129" "ENSG00000198691" "ENSG00000097007"
[25] "ENSG00000002726" "ENSG00000143322" "ENSG00000175164" "ENSG00000281879"
[29] "ENSG00000159842" "ENSG00000276016"
> fakedata <- data.frame(EnsGene = ensgs, fakestuff =rnorm(30), stringsAsFactors = FALSE)
> z <- getBM(c("ensembl_gene_id","hgnc_symbol"), "ensembl_gene_id", fakedata[,1], mart)
> head(z)
  ensembl_gene_id hgnc_symbol
1 ENSG00000002726        AOC1
2 ENSG00000090861        AARS
3 ENSG00000097007        ABL1
4 ENSG00000107331       ABCA2
5 ENSG00000114771       AADAC
6 ENSG00000121410        A1BG
> fakedata$symbol <- z[match(fakedata[,1], z[,1]),2]
> fakedata
           EnsGene  fakestuff   symbol
1  ENSG00000121410  0.4284778     A1BG
2  ENSG00000175899  0.7939349      A2M
3  ENSG00000256069 -0.7086452    A2MP1
4  ENSG00000171428  1.0021299     NAT1
5  ENSG00000156006 -1.5783433     NAT2
6  ENSG00000196136 -0.2404067 SERPINA3
7  ENSG00000114771  0.6693119    AADAC
8  ENSG00000127837  0.7599615     AAMP
9  ENSG00000129673  0.2137799    AANAT
10 ENSG00000090861 -1.1840495     AARS
11 ENSG00000183044  1.7226415     ABAT
12 ENSG00000165029  1.0943198    ABCA1
13 ENSG00000107331 -0.9202913    ABCA2
14 ENSG00000167972 -0.9597995    ABCA3
15 ENSG00000131269  1.7312147    ABCB7
16 ENSG00000204574  0.1767857    ABCF1
17 ENSG00000225989 -1.3855398    ABCF1
18 ENSG00000232169 -0.4199767    ABCF1
19 ENSG00000206490  0.1315500    ABCF1
20 ENSG00000236149 -1.1918259    ABCF1
21 ENSG00000236342  1.2702487    ABCF1
22 ENSG00000231129  1.3142160    ABCF1
23 ENSG00000198691 -0.3801780    ABCA4
24 ENSG00000097007  1.6980101     ABL1
25 ENSG00000002726  0.3474628     AOC1
26 ENSG00000143322 -0.9090020     ABL2
27 ENSG00000175164 -2.6847646      ABO
28 ENSG00000281879 -1.2566993      ABO
29 ENSG00000159842  0.7652590      ABR
30 ENSG00000276016 -0.5721807      ABR​
ADD COMMENTlink written 8 months ago by James W. MacDonald48k
0
gravatar for cherlyn.t
8 months ago by
cherlyn.t0
cherlyn.t0 wrote:

Hi,

James's method is great, but I have found the merge function to be simpler, you can merge both the converted list and your original list by = "ensembl_gene_id ", you just have to change the colname of "V1" to "ensembl_gene_id ".

I hope it helps.

 

ADD COMMENTlink written 8 months ago by cherlyn.t0
0
gravatar for Yuqia
8 months ago by
Yuqia0
Switzerland
Yuqia0 wrote:

Hi James,

Thank you very much! That sounds great! I'll try that.

Hi cherlyn, the V1 is the automatic header of the list when I use as.vector(list). But when I use read.csv to import the data, the list does not have that V1. Thank you for your input. I'll try that as well.

ADD COMMENTlink written 8 months ago by Yuqia0
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