Hi Steffen and Wolfgang,

thanks for the update and info - and all your efforts providing help with R/Bioconductor on this list.

Best regards,
Kemal


Am 14.11.2010 um 19:50 schrieb Steffen Durinck:

Hi Kemal,


The combo filter chromosome_name, start and end position is interpreted by the Ensembl BioMart as 'give everything on this chromosome between the given start and end position'.
However this combo filter is an exception to other filters, that it doesn't know what to do when you give it a list of many chromosomes and many positions.

This is not well annotated in the vignette but the current version of BioMart doesn't understand multiple locations given at once.

It is better in this case to query for all genes and there positions and then select the ones you're interested in R:

genes <- getBM(attributes = c("entrezgene","chromosome_name", "start", "end", "strand"), mart = ensembl54)

By not specifying any filter you get all positions.

I will update the vignette to reflect this info.

Cheers,
Steffen


On Sun, Nov 14, 2010 at 11:48 AM, Wolfgang Huber <whuber@embl.de<mailto:whuber@embl.de>> wrote:
Dear Kemal,

thank you for your explanation - I understand the 'conceptual' nature of your post. Just, if someone that wants to help would like to start from what you have tried and improve on it or make suggestions on it, it's more efficient if the starting points agree as much as possible.

I made some experiments with your query to the Ensembl BioMart (see attached, try different choices for 'sel'), and, like you, also could not get meaningful results out if. 'getBM' returns a huge results dataframe whose origin or rationale I fail to understand. Maybe one of the Ensembl / BioMart experts can say something?

I agree with Vince & Martin, however, that the GenomicRanges-based approach suggested by Vince is much more appropriate here, for many reasons, including flexibility and speed.

       Best wishes
       Wolfgang


Il Nov/13/10 1:19 AM, Kemal Akat ha scritto:

Dear Vincent and Martin,

thank you for your help and explanations. I will try your suggestions.

Dear Wolfgang,

sorry if the info I posted was incomplete. It was more a semantic explanation than a technical one. I realized the incorrect syntax, but that was just a typo (as I couldn't copy and paste back then). I'll try to be more precise in the future.

For the sake of completeness here is the actual code I was running:

1) with one filter, referring to the column of the data frame

options(width = 800, max.print = 5E5)
library(biomaRt)
ensembl54<- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "may2009.archive.ensembl.org<http://may2009.archive.ensembl.org/>", path = "/biomart/martservice", archive = FALSE)
tdp<- read.delim("/Users/Kemal/Desktop/Projects/biomaRt/tdp.txt", row.names = 1)
genes<- getBM(attributes = "entrezgene", filters = c("chromosomal_region"), values = list(tdp$Chromosomal_Location), mart = ensembl54)
genes
      entrezgene
1           6964
2         651536
3         445347
4           3492
5      100133739
6         652494
...
19731      55657
19732     267002
19733     692312
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-3 XML_3.2-0


2) with multiple filters and the localization info splitted into 4 separate vectors

options(width = 800, max.print = 5E5) # change display settings to allow larger data frames, modify as needed
library(biomaRt) # load the biomaRt package
#ensembl<- useMart("ensembl", dataset = "hsapiens_gene_ensembl") # to assign the variable ensembl (or else) to hg19, NCBI build 37
ensembl54<- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "may2009.archive.ensembl.org<http://may2009.archive.ensembl.org/>", path = "/biomart/martservice", archive = FALSE) # to use the hg18, NCBI build 36

chromosome<-c(2, 1, 8, 17, 12, 10, 21, 2, 7, 16, 5, 4, 1, 19, 13, 13, 10, 7, 15, 7, 2, 12, 21, 20, 5, 11, 15, 12, 17, 3, 17, 14, 19, 13, 6, 14, 11, 13, 2, 20, 7, 10, 1, 16, "X", 22, 20, 1, 3, 8, 4, 1, 6, 15, 17, 4, 12, 7, 1, 14, 12, 17, 12, 6, 9, 22, "X", 7, 12, 10, 19, 5, 1, 8, 11, 8, 19, 7, 6, 5, 1, 6, 9, 19, 10, "X", 3, 5, 13, 17, 20, 3, 16, 5, 13, 12, 15, 19, 4, 16, 10, 8, 7, 7, 12, 6, 11, 21, 17, "X", 15, 10, 16, 15, 9, 5, 2, 6, 12, 5, 14, 14, 6, 6, 15, 4, 1, 9, 8, 1, 5, "X", 11, 2, 1, 19, 2, 2, 13, 1, 17, 13, "X", 13, 7, 11, 3, "X", 15, 17, 22, 11, 16, 19, 7, 2, 13, 9, 14, 12, 1)

strand<- c(1, -1, -1, -1, -1, 1, 1, 1, 1, 1, 1, 1, 1, -1, 1, 1, 1, 1, 1, -1, 1, -1, -1, -1, 1, -1, -1, -1, 1, 1, -1, 1, -1, -1, 1, 1, -1, 1, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1, -1, -1, 1, 1, 1, -1, 1, -1, 1, 1, 1, 1, 1, 1, 1, 1, 1, -1, -1, 1, 1, -1, -1, -1, -1, 1, -1, 1, -1, 1, -1, 1, -1, -1, 1, -1, 1, -1, -1, 1, -1, 1, 1, -1, -1, 1, -1, -1, 1, -1, 1, 1, 1, 1, 1, -1, 1, -1, 1, 1, -1, 1, 1, 1, 1, -1, 1, 1, 1, 1, 1, -1, 1, -1, -1, -1, -1, 1, 1, 1, -1, -1, 1, 1, -1, -1, -1, -1, -1, -1, -1, 1, 1, -1, -1, 1, 1, -1, 1, -1, -1, -1, 1, -1, 1, 1, -1, 1, 1, -1)

start<- c(74295624, 203949843, 103464182, 53272097, 11150173, 52616450, 29638098, 160316091, 26218430, 73763529, 118611423, 78176046, 39566219, 45430361, 34823356, 114106490, 85902288, 55407132, 97080019, 97322520, 241940312, 49774225, 43149920, 1298551, 71540977, 2967925, 75125438, 107566872, 32012029, 50130463, 24612590, 103222346, 49628998, 76795050,47700337, 61273382, 64288817, 99433818, 86857893, 60954640, 121562796, 102024852, 233341511, 46963400, 54115224, 17405158, 33706984, 233341179, 11574528, 117938795, 100202920, 191280320, 89641039, 91241813, 27712528, 72107017, 45043151, 115686015, 227526472, 59794222, 132193041, 2534782, 49500468, 64462329, 19040649, 34020658, 118261386, 5071002,47616321, 101146860, 41419808, 145858601, 9912662, 109329554, 47446160, 130922997, 42311362, 135263153, 64348945, 32179718, 224044250, 112127969, 37126090, 41697757, 7442786, 24005946, 52264406, 154175486, 76478566, 20845822, 30384091, 9561760, 55844512, 65510903, 73435394, 52920938!

 , 42797538, 45273560, 174489559, 55535115, 847112, 26283582,79686310, 138640447, 751963, 124334398, 122435615, 29638867, 5277351, 46804967, 39560795, 89503999, 55844568, 42797166, 113346669, 139476285, 74236497, 43716256, 52725397, 137763505, 31647833, 101463626, 136622538, 76608878, 66287317, 174489713, 32145213, 114023332, 61632141, 160759702, 56575893, 73723822, 92851504, 74295579, 20108627, 51970080,86384720, 174692895, 76479389, 233342144, 19819930, 47962168, 70434946, 33344305, 135285934, 64288869, 143115273, 100555421, 40493944, 44486723, 37016836, 27475187, 14437226, 40184189, 104928588, 38862574, 96917747, 114023291, 89944103, 67952950, 223656250)

end<- c(74295644, 203949866, 103464207, 53272117, 11150194, 52616474, 29638121, 160316115, 26218451, 73763550, 118611442, 78176077, 39566244, 45430401, 34823379, 114106513, 85902314, 55407154, 97080040, 97322541, 241940335, 49774248, 43149944, 1298573, 71540997, 2967950, 75125461, 107566904, 32012052, 50130483, 24612615, 103222367, 49629021, 76795071, 47700356, 61273403, 64288842, 99433838, 86857915, 60954662, 121562817, 102024873, 233341535, 46963421, 54115248, 17405178, 33707009, 233341202, 11574549, 117938820, 100202946, 191280339, 89641061, 91241835, 27712550, 72107038, 45043175, 115686058, 227526491, 59794245, 132193064, 2534802, 49500489, 64462352, 19040675, 34020682, 118261409, 5071024, 47616347, 101146884, 41419832, 145858626, 9912686, 109329575, 47446181, 130923017, 42311383, 135263177, 64348968, 32179741, 224044275, 112127989, 37126110, 41697783, 7442807, 24005968, 52264426, 154175508, 76478587, 20845844, 30384113, 9561782, 55844532, 65510922, 73435415, 52920963!

 , 42797563, 45273580, 174489628, 55535135, 847134, 26283606, 79686336, 138640468, 751985, 124334422, 122435636, 29638895, 5277374, 46804991, 39560819, 89504022, 55844595, 42797186, 113346688, 139476306, 74236521, 43716279, 52725418, 137763531, 31647855, 101463647, 136622560, 76608900, 66287361, 174489736, 32145234, 114023358, 61632162, 160759726, 56575914, 73723844, 92851527, 74295600, 20108650, 51970105, 86384744, 174692915, 76479410, 233342163, 19819951, 47962190, 70434970, 33344326, 135285963, 64288896, 143115294, 100555442, 40493968, 44486745, 37016858, 27475207, 14437254, 40184209, 104928610, 38862598, 96917795, 114023316, 89944124, 67952970, 223656273)

genes<- getBM(attributes = "entrezgene", filters = c("chromosome_name", "start", "end", "strand"), values = list(chromosome, start, end, strand), mart = ensembl54)
genes
      entrezgene
1           6964
2         651536
3         445347
4           3492
...
19073      10806
19074      10000
19075     692312
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-3 XML_3.2-0


Kind regards,
Kemal


Am 12.11.2010 um 09:16 schrieb Martin Morgan:

On 11/12/2010 04:18 AM, Vincent Carey wrote:
tx18 = transcripts(hg18.txdb)
kg = values(tx18[ findOverlaps(kem,tx18)@matchMatrix[,2] ])$tx_name

Better to use the accessor matchMatrix(findOveralaps(kem, tx18))

Martin

--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch<mailto:Bioconductor@stat.math.ethz.ch>
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch<mailto:Bioconductor@stat.math.ethz.ch>
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



	[[alternative HTML version deleted]]

