How to transform 'chromosome start end' to 'band' in batch using biomaRt？

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Yufang Li

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May 28, 2019, 8:43:18 AM5/28/19

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Hi，

I want to transform 'chromosome start end' to 'band' in batch using biomaRt now. But I met some questions. Could you help me ?

I refer to the examples on the user manual.

getBM(attributes = c('affy_hg_u133_plus_2','ensembl_gene_id'), filters = c('chromosome_name','start','end'), values = list(16,1100000,1250000), mart = ensembl)

But this example can not transform in batch. There are 328 items needed to annotate.

My data structure:

seqnames start end width strand no.cpgs minfdr Stouffer maxbetafc meanbetafc

1 16 54971700 54973047 1348 * 5 0.00e+00 0.00e+00 0.3311636 0.28623709

2 14 36992001 36993517 1517 * 4 2.93e-235 2.50e-278 0.3493025 0.32264970

3 6 31650760 31651158 399 * 7 8.20e-288 3.14e-256 0.2683500 0.23795246

4 17 79004850 79005386 537 * 3 7.45e-249 1.69e-202 0.3201577 0.29638743

5 10 134150489 134150690 202 * 4 1.88e-232 1.34e-197 0.2779639 0.26302729

6 3 169384410 169384648 239 * 3 1.50e-234 7.84e-186 0.3797378 0.30127753

7 1 151810485 151811364 880 * 6 2.08e-188 1.18e-164 0.2746188 0.23411387

8 7 5271516 5271655 140 * 2 2.54e-212 7.38e-163 0.3677478 0.34913817

9 16 54316049 54317413 1365 * 4 8.52e-184 2.45e-162 0.3459313 0.26682181

10 5 37834958 37836246 1289 * 5 1.35e-178 8.61e-155 0.2931416 0.21486234

11 7 36764019 36764140 122 * 2 9.41e-197 2.13e-148 -0.3248119 -0.28964118

12 12 16762789 16762831 43 * 2 2.69e-173 8.30e-137 0.3245738 0.31208577

13 16 68676557 68676806 250 * 2 4.21e-156 9.80e-128 0.2981041 0.28468263

14 1 247712237 247712239 3 * 2 1.69e-154 1.43e-126 -0.2896461 -0.28435472

15 5 2747922 2748369 448 * 2 7.63e-136 2.13e-113 0.2947875 0.28194606

16 11 86383696 86383761 66 * 2 3.24e-130 1.30e-109 0.2938009 0.26314046

17 16 4714794 4714815 22 * 2 2.37e-129 3.62e-109 0.2962017 0.28677182

18 19 58220295 58220818 524 * 8 3.68e-112 3.14e-108 0.1722510 0.15602547

19 1 147782116 147782452 337 * 2 7.91e-128 3.76e-108 0.2651204 0.26211464

20 19 13135662 13135808 147 * 2 1.46e-127 7.33e-108 0.2977374 0.27440837

21 10 77155376 77156421 1046 * 4 9.50e-92 3.01e-105 0.2826025 0.23205180

22 12 30976001 30976016 16 * 2 1.95e-122 2.96e-104 0.2653739 0.25972562

23 15 89951787 89953295 1509 * 4 1.25e-87 1.92e-102 0.1948644 0.17701206

24 12 58021295 58021917 623 * 4 1.00e-110 3.62e-100 0.2756699 0.20133960

25 22 30476206 30476452 247 * 3 4.68e-110 1.28e-98 0.2147699 0.18921464

26 12 54408664 54409599 936 * 7 5.71e-104 5.27e-98 0.1720937 0.14245105

27 6 10416007 10416508 502 * 4 2.52e-102 1.98e-95 -0.2120803 -0.17534331

28 7 96650096 96650192 97 * 3 7.07e-113 3.65e-95 0.2560395 0.21009693

29 7 96642096 96643508 1413 * 4 1.46e-105 3.09e-92 0.2656333 0.18161992

30 3 156324038 156324118 81 * 2 7.00e-106 4.97e-92 0.2429422 0.23746324

31 12 47219737 47219920 184 * 5 6.61e-95 1.09e-90 0.2079795 0.17331125

32 2 172953134 172953925 792 * 4 7.05e-115 2.85e-89 0.2600936 0.18543391

33 6 10420798 10422322 1525 * 5 1.04e-82 1.48e-87 0.2163537 0.16366814

34 6 7540834 7541066 233 * 3 2.00e-95 4.06e-87 0.2151257 0.21056723

35 2 175193377 175193551 175 * 2 4.88e-107 9.56e-87 0.2864994 0.26058300

36 1 226187852 226187876 25 * 2 4.13e-95 1.98e-83 0.2609258 0.24550333

37 5 2754753 2755540 788 * 2 4.75e-74 6.31e-82 0.3180281 0.27040688

38 15 89949617 89949776 160 * 2 3.59e-92 1.91e-81 0.2766399 0.24868424

And I try to write my code.

DMRS_Band=getBM(attributes = c("chromosome_name", "start_position","end_position", "band"), filters = c('chromosome_name','start','end'), values = list(chromosome_name=Methy_5_DMRs_S1_S3_annotation$seqnames,start=Methy_5_DMRs_S1_S3_annotation$start,end=Methy_5_DMRs_S1_S3_annotation$end), mart = mart)

But the annotation results return 55512 records.

I think the result should be return 328 records in theory. But there are 55512 records returned. So think there may be error in my code.

This follows an example.

chromosome_name start_position end_position band 1 1 16873708 16873851 p36.13 2 1 12507246 12507397 p36.21 3 1 202070841 202070943 q32.1 4 1 45592722 45592814 p34.1 5 1 23370254 23370346 p36.12 6 1 12166943 12167038 p36.22 7 1 167998660 167998726 q24.2 8 1 32086949 32087007 p35.2 9 1 171101728 171101806 q24.3 10 1 28648600 28648733 p35.3 11 1 62078786 62078859 p31.3 12 1 220117853 220117962 q41 13 1 148334479 148334554 q21.2

I want to solve this problem. So I write a loop to annotate one by one. But there are another error. We can not call biomaRt API for many times. Otherwise there will be error.

My code:

DMRs_Final<-data.frame(seqnames=c(NA), start=c(NA), end=c(NA), width=c(NA), strand=c(NA), no.cpgs=c(NA), minfdr=c(NA), Stouffer=c(NA), maxbetafc=c(NA), meanbetafc=c(NA), overlapping.promoters=c(NA),chromosome_name=c(NA), start_position=c(NA), end_position=c(NA), band=c(NA))

for(i in 1:nrow(Methy_5_DMRs_S1_S3_annotation)){ DMRs_original=Methy_5_DMRs_S1_S3_annotation[i,] DMRS_Band=getBM(attributes = c("chromosome_name", "start_position","end_position", "band"), filters = c('chromosome_name','start','end'), values = list(DMRs_original$seqnames,DMRs_original$start,DMRs_original$end), mart = mart) if(nrow(DMRS_Band)==0){ i=i+1 }else{ DMRs_merge=cbind(DMRs_original,DMRS_Band) DMRs_Final=rbind(DMRs_Final,DMRs_merge) } }

There follows the error.

Error in getBM(attributes = c("chromosome_name", "start_position", "end_position", :

The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.

Please report this on the support site at http://support.bioconductor.org

So, could you tell me to how to transform 'chromosome start end' to 'band' in batch using biomaRt？