Question: mouse SNPs
0
gravatar for Glazko, Galina
9.3 years ago by
Glazko, Galina350 wrote:
Dear list, I have annotation question and just hope that someone had already similar problem and would be willing to share the experience. I have about 100 mouse SNPs in the format: Chromosome number SNP coordinate (for example:) 16 69067865 I need to annotate them, in order to understand whether they are functional or not. I can go one-by-one through UCSC (http://www.genome.ucsc.edu/) and annotate them, but I hope that may be someone already did something similar and has better ideas about how to do it faster, probably using Bioconductor? And also, may be there are specific resources available for mouse SNPs annotation? There is mouse HapMap, but it is just a collection of SNPs in different strains and nothing else. I would really appreciate your suggestions! best regards Galina [[alternative HTML version deleted]]
snp annotation go hapmap annotate • 829 views
ADD COMMENTlink modified 9.3 years ago • written 9.3 years ago by Glazko, Galina350
Answer: mouse SNPs
0
gravatar for Vincent J. Carey, Jr.
9.3 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
What do you mean by "annotate"? Your best bet for a programmatic attack is probably biomaRt library(biomaRt) listMarts() mm = useMart("snp") listDatasets(mm) ds = useDataset("mmusculus_snp", mart=mm) listAttributes(ds) then the fun begins with getBM... On Wed, Sep 8, 2010 at 1:04 PM, Glazko, Galina <galina_glazko at="" urmc.rochester.edu=""> wrote: > Dear list, > > I have annotation question and just hope that someone had already similar problem and > would be willing to share the experience. > > I have about 100 mouse SNPs in the format: > > Chromosome number ? ? SNP coordinate > (for example:) > 16 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 69067865 > > I need to annotate them, in order to understand whether they are functional or not. > I can go one-by-one through UCSC (http://www.genome.ucsc.edu/) > and annotate them, but I hope that may be someone already did something similar > and has better ideas about how to do it faster, probably using Bioconductor? > And also, may be there are specific resources available for mouse SNPs annotation? > There is mouse HapMap, but it is just a collection of SNPs in different strains and nothing else. > > I would really appreciate your suggestions! > best regards > Galina > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 9.3 years ago by Vincent J. Carey, Jr.6.3k
Answer: mouse SNPs
0
gravatar for Julie Zhu
9.3 years ago by
Julie Zhu4.1k
United States
Julie Zhu4.1k wrote:
Hi Galina, You could use the annotatePeakInBatch function in ChIPpeakAnno package to annotate the SNP to the nearest gene and whether the SNP is inside the gene or not. Best regards, Julie On 9/8/10 1:04 PM, "Glazko, Galina" <galina_glazko at="" urmc.rochester.edu=""> wrote: > Dear list, > > I have annotation question and just hope that someone had already similar > problem and > would be willing to share the experience. > > I have about 100 mouse SNPs in the format: > > Chromosome number SNP coordinate > (for example:) > 16 69067865 > > I need to annotate them, in order to understand whether they are functional or > not. > I can go one-by-one through UCSC (http://www.genome.ucsc.edu/) > and annotate them, but I hope that may be someone already did something > similar > and has better ideas about how to do it faster, probably using Bioconductor? > And also, may be there are specific resources available for mouse SNPs > annotation? > There is mouse HapMap, but it is just a collection of SNPs in different > strains and nothing else. > > I would really appreciate your suggestions! > best regards > Galina > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 9.3 years ago by Julie Zhu4.1k
Answer: mouse SNPs
0
gravatar for Glazko, Galina
9.3 years ago by
Glazko, Galina350 wrote:
Dear Vincent and Julie, thank you for the helpful hints! Julie, annotatePeakInBatch works great! But now I have another question: I am trying to annotate these feautures I got back (using Annotation = getAnnotation(mart, featureType="Exon")) and I have this table: space start end width names peak strand feature 1 17 45883787 45883887 101 mm37-17-45883787 ENSMUSE00000844234 mm37-17-45883787 1 ENSMUSE00000844234 2 17 29434504 29434604 101 NES16571232 ENSMUSE00000813877 NES16571232 1 ENSMUSE00000813877 3 17 29428231 29428331 101 NES16571402 ENSMUSE00000421676 NES16571402 1 ENSMUSE00000421676 4 17 31949127 31949227 101 NES15760823 ENSMUSE00000493746 NES15760823 -1 ENSMUSE00000493746 5 17 31948263 31948363 101 NES15760902 ENSMUSE00000493746 NES15760902 -1 ENSMUSE00000493746 6 17 31948318 31948418 101 NES15760903 ENSMUSE00000493746 NES15760903 -1 ENSMUSE00000493746 7 17 29329081 29329181 101 NES16573923 ENSMUSE00000762871 NES16573923 -1 ENSMUSE00000762871 8 17 29328546 29328646 101 NES16573940 ENSMUSE00000762871 NES16573940 -1 ENSMUSE00000762871 9 17 29328568 29328668 101 NES16573943 ENSMUSE00000762871 NES16573943 -1 ENSMUSE00000762871 10 17 29327513 29327613 101 NES16573962 ENSMUSE00000762871 NES16573962 -1 ENSMUSE00000762871 11 17 29327728 29327828 101 NES16573970 ENSMUSE00000762871 NES16573970 -1 ENSMUSE00000762871 12 17 29327208 29327308 101 NES16573987 ENSMUSE00000762871 NES16573987 -1 ENSMUSE00000762871 13 17 29327324 29327424 101 NES16573988 ENSMUSE00000762871 NES16573988 -1 ENSMUSE00000762871 14 17 29326956 29327056 101 NES16573997 ENSMUSE00000762871 NES16573997 -1 ENSMUSE00000762871 15 17 29316818 29316918 101 NES16574121 ENSMUSE00000726199 NES16574121 -1 ENSMUSE00000726199 I thought that these identifiers (e.g. 'ENSMUSE00000844234') are ensembl genes and wanted to get back gene names and descriptions. Apparently I was wrong: if I try e.g. getBM(attributes=c("mgi_description","mgi_symbol"),filters='ensembl_ge ne_id',values=c("ENSMUSE00000844234"), mart=mart) I get nothing back (same with transcripts and exons). Could you please let me know what is their ensembl name? (from listFilters(mart)?). thank you! best regards Galina [[alternative HTML version deleted]]
ADD COMMENTlink written 9.3 years ago by Glazko, Galina350
Galina, Since you used Exon as featureType, the feature column is the ensembl_exon_id instead of ensembl_gene ID. Kind regards, Julie On 9/9/10 1:53 PM, "Glazko, Galina" <galina_glazko@urmc.rochester.edu> wrote: Dear Vincent and Julie, thank you for the helpful hints! Julie, annotatePeakInBatch works great! But now I have another question: I am trying to annotate these feautures I got back (using Annotation = getAnnotation(mart, featureType="Exon")) and I have this table: space start end width names peak strand feature 1 17 45883787 45883887 101 mm37-17-45883787 ENSMUSE00000844234 mm37-17-45883787 1 ENSMUSE00000844234 2 17 29434504 29434604 101 NES16571232 ENSMUSE00000813877 NES16571232 1 ENSMUSE00000813877 3 17 29428231 29428331 101 NES16571402 ENSMUSE00000421676 NES16571402 1 ENSMUSE00000421676 4 17 31949127 31949227 101 NES15760823 ENSMUSE00000493746 NES15760823 -1 ENSMUSE00000493746 5 17 31948263 31948363 101 NES15760902 ENSMUSE00000493746 NES15760902 -1 ENSMUSE00000493746 6 17 31948318 31948418 101 NES15760903 ENSMUSE00000493746 NES15760903 -1 ENSMUSE00000493746 7 17 29329081 29329181 101 NES16573923 ENSMUSE00000762871 NES16573923 -1 ENSMUSE00000762871 8 17 29328546 29328646 101 NES16573940 ENSMUSE00000762871 NES16573940 -1 ENSMUSE00000762871 9 17 29328568 29328668 101 NES16573943 ENSMUSE00000762871 NES16573943 -1 ENSMUSE00000762871 10 17 29327513 29327613 101 NES16573962 ENSMUSE00000762871 NES16573962 -1 ENSMUSE00000762871 11 17 29327728 29327828 101 NES16573970 ENSMUSE00000762871 NES16573970 -1 ENSMUSE00000762871 12 17 29327208 29327308 101 NES16573987 ENSMUSE00000762871 NES16573987 -1 ENSMUSE00000762871 13 17 29327324 29327424 101 NES16573988 ENSMUSE00000762871 NES16573988 -1 ENSMUSE00000762871 14 17 29326956 29327056 101 NES16573997 ENSMUSE00000762871 NES16573997 -1 ENSMUSE00000762871 15 17 29316818 29316918 101 NES16574121 ENSMUSE00000726199 NES16574121 -1 ENSMUSE00000726199 I thought that these identifiers (e.g. 'ENSMUSE00000844234') are ensembl genes and wanted to get back gene names and descriptions. Apparently I was wrong: if I try e.g. getBM(attributes=c("mgi_description","mgi_symbol"),filters='ensembl_ge ne_id',values=c("ENSMUSE00000844234"), mart=mart) I get nothing back (same with transcripts and exons). Could you please let me know what is their ensembl name? (from listFilters(mart)?). thank you! best regards Galina [[alternative HTML version deleted]]
ADD REPLYlink written 9.3 years ago by Julie Zhu4.1k
Julie, yes I tried this but it did not work: > getBM(attributes=c("chromosome_name"),filters="ensembl_exon_id",valu es=c("ENSMUSE00000844234"), mart=mart) Error in getBM(attributes = c("chromosome_name"), filters = "ensembl_exon_id", : Invalid filters(s): ensembl_exon_id Please use the function 'listFilters' to get valid filter names > I do not understand why. best regards Galina ________________________________ From: Zhu, Julie [Julie.Zhu@umassmed.edu] Sent: Thursday, September 09, 2010 2:07 PM To: Glazko, Galina; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] mouse SNPs annotation with ChIPpeakAnno Galina, Since you used Exon as featureType, the feature column is the ensembl_exon_id instead of ensembl_gene ID. Kind regards, Julie On 9/9/10 1:53 PM, "Glazko, Galina" <galina_glazko@urmc.rochester.edu<urlblockederror.aspx>> wrote: Dear Vincent and Julie, thank you for the helpful hints! Julie, annotatePeakInBatch works great! But now I have another question: I am trying to annotate these feautures I got back (using Annotation = getAnnotation(mart, featureType="Exon")) and I have this table: space start end width names peak strand feature 1 17 45883787 45883887 101 mm37-17-45883787 ENSMUSE00000844234 mm37-17-45883787 1 ENSMUSE00000844234 2 17 29434504 29434604 101 NES16571232 ENSMUSE00000813877 NES16571232 1 ENSMUSE00000813877 3 17 29428231 29428331 101 NES16571402 ENSMUSE00000421676 NES16571402 1 ENSMUSE00000421676 4 17 31949127 31949227 101 NES15760823 ENSMUSE00000493746 NES15760823 -1 ENSMUSE00000493746 5 17 31948263 31948363 101 NES15760902 ENSMUSE00000493746 NES15760902 -1 ENSMUSE00000493746 6 17 31948318 31948418 101 NES15760903 ENSMUSE00000493746 NES15760903 -1 ENSMUSE00000493746 7 17 29329081 29329181 101 NES16573923 ENSMUSE00000762871 NES16573923 -1 ENSMUSE00000762871 8 17 29328546 29328646 101 NES16573940 ENSMUSE00000762871 NES16573940 -1 ENSMUSE00000762871 9 17 29328568 29328668 101 NES16573943 ENSMUSE00000762871 NES16573943 -1 ENSMUSE00000762871 10 17 29327513 29327613 101 NES16573962 ENSMUSE00000762871 NES16573962 -1 ENSMUSE00000762871 11 17 29327728 29327828 101 NES16573970 ENSMUSE00000762871 NES16573970 -1 ENSMUSE00000762871 12 17 29327208 29327308 101 NES16573987 ENSMUSE00000762871 NES16573987 -1 ENSMUSE00000762871 13 17 29327324 29327424 101 NES16573988 ENSMUSE00000762871 NES16573988 -1 ENSMUSE00000762871 14 17 29326956 29327056 101 NES16573997 ENSMUSE00000762871 NES16573997 -1 ENSMUSE00000762871 15 17 29316818 29316918 101 NES16574121 ENSMUSE00000726199 NES16574121 -1 ENSMUSE00000726199 I thought that these identifiers (e.g. 'ENSMUSE00000844234') are ensembl genes and wanted to get back gene names and descriptions. Apparently I was wrong: if I try e.g. getBM(attributes=c("mgi_description","mgi_symbol"),filters='ensembl_ge ne_id',values=c("ENSMUSE00000844234"), mart=mart) I get nothing back (same with transcripts and exons). Could you please let me know what is their ensembl name? (from listFilters(mart)?). thank you! best regards Galina [[alternative HTML version deleted]]
ADD REPLYlink written 9.3 years ago by Glazko, Galina350
Hi Galina, Those are Ensembl exon identifiers. Unfortunately there is no exon idenfier filter in the Ensembl mouse BioMart so you cannot use an exon identifier directly as input for a getBM query. You could however get an exon to gene id mapping as follows: mouse=useMart("ensembl",dataset="mmusculus_gene_ensembl") map = getBM(c("ensembl_gene_id","ensembl_exon_id"),mart=mouse) You should get: > head(map) ensembl_gene_id ensembl_exon_id 1 ENSMUSG00000087647 ENSMUSE00000751459 2 ENSMUSG00000087647 ENSMUSE00000817668 3 ENSMUSG00000087647 ENSMUSE00000751482 4 ENSMUSG00000081805 ENSMUSE00000712902 5 ENSMUSG00000081824 ENSMUSE00000719687 6 ENSMUSG00000086074 ENSMUSE00000808926 Which you can use to map from exon id to ensembl gene id Note that if you want symbols and a description you could do: map = getBM(c("mgi_description", "mgi_symbol","ensembl_exon_id"),mart=mouse) (This will take a while to download) Cheers, Steffen On Thu, Sep 9, 2010 at 11:15 AM, Glazko, Galina < Galina_Glazko@urmc.rochester.edu> wrote: > Julie, > yes I tried this but it did not work: > > > getBM(attributes=c("chromosome_name"),filters="ensembl_exon_id",valu es=c("ENSMUSE00000844234"), > mart=mart) > Error in getBM(attributes = c("chromosome_name"), filters = > "ensembl_exon_id", : > Invalid filters(s): ensembl_exon_id > Please use the function 'listFilters' to get valid filter names > > > I do not understand why. > best regards > Galina > ________________________________ > From: Zhu, Julie [Julie.Zhu@umassmed.edu] > Sent: Thursday, September 09, 2010 2:07 PM > To: Glazko, Galina; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] mouse SNPs annotation with ChIPpeakAnno > > Galina, > > Since you used Exon as featureType, the feature column is the > ensembl_exon_id instead of ensembl_gene ID. > > Kind regards, > > Julie > > > On 9/9/10 1:53 PM, "Glazko, Galina" <galina_glazko@urmc.rochester.edu<urlblockederror.aspx>> > wrote: > > Dear Vincent and Julie, > > thank you for the helpful hints! > > Julie, annotatePeakInBatch works great! > But now I have another question: > I am trying to annotate these feautures I got back (using Annotation = > getAnnotation(mart, featureType="Exon")) > and I have this table: > space start end width names > peak strand feature > 1 17 45883787 45883887 101 mm37-17-45883787 ENSMUSE00000844234 > mm37-17-45883787 1 ENSMUSE00000844234 > 2 17 29434504 29434604 101 NES16571232 ENSMUSE00000813877 > NES16571232 1 ENSMUSE00000813877 > 3 17 29428231 29428331 101 NES16571402 ENSMUSE00000421676 > NES16571402 1 ENSMUSE00000421676 > 4 17 31949127 31949227 101 NES15760823 ENSMUSE00000493746 > NES15760823 -1 ENSMUSE00000493746 > 5 17 31948263 31948363 101 NES15760902 ENSMUSE00000493746 > NES15760902 -1 ENSMUSE00000493746 > 6 17 31948318 31948418 101 NES15760903 ENSMUSE00000493746 > NES15760903 -1 ENSMUSE00000493746 > 7 17 29329081 29329181 101 NES16573923 ENSMUSE00000762871 > NES16573923 -1 ENSMUSE00000762871 > 8 17 29328546 29328646 101 NES16573940 ENSMUSE00000762871 > NES16573940 -1 ENSMUSE00000762871 > 9 17 29328568 29328668 101 NES16573943 ENSMUSE00000762871 > NES16573943 -1 ENSMUSE00000762871 > 10 17 29327513 29327613 101 NES16573962 ENSMUSE00000762871 > NES16573962 -1 ENSMUSE00000762871 > 11 17 29327728 29327828 101 NES16573970 ENSMUSE00000762871 > NES16573970 -1 ENSMUSE00000762871 > 12 17 29327208 29327308 101 NES16573987 ENSMUSE00000762871 > NES16573987 -1 ENSMUSE00000762871 > 13 17 29327324 29327424 101 NES16573988 ENSMUSE00000762871 > NES16573988 -1 ENSMUSE00000762871 > 14 17 29326956 29327056 101 NES16573997 ENSMUSE00000762871 > NES16573997 -1 ENSMUSE00000762871 > 15 17 29316818 29316918 101 NES16574121 ENSMUSE00000726199 > NES16574121 -1 ENSMUSE00000726199 > > I thought that these identifiers (e.g. 'ENSMUSE00000844234') are ensembl > genes and wanted to get back gene names and descriptions. > Apparently I was wrong: if I try e.g. > > getBM(attributes=c("mgi_description","mgi_symbol"),filters='ensembl_ gene_id',values=c("ENSMUSE00000844234"), > mart=mart) > > I get nothing back (same with transcripts and exons). Could you please let > me know what is their ensembl name? > (from listFilters(mart)?). > thank you! > best regards > Galina > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > 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]]
ADD REPLYlink written 9.3 years ago by Steffen500
Steffen, Thank you! This works perfectly fine! Best regards Galina ________________________________ From: Steffen Durinck [mailto:sdurinck@lbl.gov] Sent: Thursday, September 09, 2010 2:28 PM To: Glazko, Galina Cc: Zhu, Julie; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] mouse SNPs annotation with ChIPpeakAnno Hi Galina, Those are Ensembl exon identifiers. Unfortunately there is no exon idenfier filter in the Ensembl mouse BioMart so you cannot use an exon identifier directly as input for a getBM query. You could however get an exon to gene id mapping as follows: mouse=useMart("ensembl",dataset="mmusculus_gene_ensembl") map = getBM(c("ensembl_gene_id","ensembl_exon_id"),mart=mouse) You should get: > head(map) ensembl_gene_id ensembl_exon_id 1 ENSMUSG00000087647 ENSMUSE00000751459 2 ENSMUSG00000087647 ENSMUSE00000817668 3 ENSMUSG00000087647 ENSMUSE00000751482 4 ENSMUSG00000081805 ENSMUSE00000712902 5 ENSMUSG00000081824 ENSMUSE00000719687 6 ENSMUSG00000086074 ENSMUSE00000808926 Which you can use to map from exon id to ensembl gene id Note that if you want symbols and a description you could do: map = getBM(c("mgi_description", "mgi_symbol","ensembl_exon_id"),mart=mouse) (This will take a while to download) Cheers, Steffen On Thu, Sep 9, 2010 at 11:15 AM, Glazko, Galina <galina_glazko@urmc.ro chester.edu<mailto:galina_glazko@urmc.rochester.edu="">> wrote: Julie, yes I tried this but it did not work: > getBM(attributes=c("chromosome_name"),filters="ensembl_exon_id",valu es=c("ENSMUSE00000844234"), mart=mart) Error in getBM(attributes = c("chromosome_name"), filters = "ensembl_exon_id", : Invalid filters(s): ensembl_exon_id Please use the function 'listFilters' to get valid filter names > I do not understand why. best regards Galina ________________________________ From: Zhu, Julie [Julie.Zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>] Sent: Thursday, September 09, 2010 2:07 PM To: Glazko, Galina; bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch> Subject: Re: [BioC] mouse SNPs annotation with ChIPpeakAnno Galina, Since you used Exon as featureType, the feature column is the ensembl_exon_id instead of ensembl_gene ID. Kind regards, Julie On 9/9/10 1:53 PM, "Glazko, Galina" <galina_glazko@urmc.rochester.edu< mailto:galina_glazko@urmc.rochester.edu=""><urlblockederror.aspx>> wrote: Dear Vincent and Julie, thank you for the helpful hints! Julie, annotatePeakInBatch works great! But now I have another question: I am trying to annotate these feautures I got back (using Annotation = getAnnotation(mart, featureType="Exon")) and I have this table: space start end width names peak strand feature 1 17 45883787 45883887 101 mm37-17-45883787 ENSMUSE00000844234 mm37-17-45883787 1 ENSMUSE00000844234 2 17 29434504 29434604 101 NES16571232 ENSMUSE00000813877 NES16571232 1 ENSMUSE00000813877 3 17 29428231 29428331 101 NES16571402 ENSMUSE00000421676 NES16571402 1 ENSMUSE00000421676 4 17 31949127 31949227 101 NES15760823 ENSMUSE00000493746 NES15760823 -1 ENSMUSE00000493746 5 17 31948263 31948363 101 NES15760902 ENSMUSE00000493746 NES15760902 -1 ENSMUSE00000493746 6 17 31948318 31948418 101 NES15760903 ENSMUSE00000493746 NES15760903 -1 ENSMUSE00000493746 7 17 29329081 29329181 101 NES16573923 ENSMUSE00000762871 NES16573923 -1 ENSMUSE00000762871 8 17 29328546 29328646 101 NES16573940 ENSMUSE00000762871 NES16573940 -1 ENSMUSE00000762871 9 17 29328568 29328668 101 NES16573943 ENSMUSE00000762871 NES16573943 -1 ENSMUSE00000762871 10 17 29327513 29327613 101 NES16573962 ENSMUSE00000762871 NES16573962 -1 ENSMUSE00000762871 11 17 29327728 29327828 101 NES16573970 ENSMUSE00000762871 NES16573970 -1 ENSMUSE00000762871 12 17 29327208 29327308 101 NES16573987 ENSMUSE00000762871 NES16573987 -1 ENSMUSE00000762871 13 17 29327324 29327424 101 NES16573988 ENSMUSE00000762871 NES16573988 -1 ENSMUSE00000762871 14 17 29326956 29327056 101 NES16573997 ENSMUSE00000762871 NES16573997 -1 ENSMUSE00000762871 15 17 29316818 29316918 101 NES16574121 ENSMUSE00000726199 NES16574121 -1 ENSMUSE00000726199 I thought that these identifiers (e.g. 'ENSMUSE00000844234') are ensembl genes and wanted to get back gene names and descriptions. Apparently I was wrong: if I try e.g. getBM(attributes=c("mgi_description","mgi_symbol"),filters='ensembl_ge ne_id',values=c("ENSMUSE00000844234"), mart=mart) I get nothing back (same with transcripts and exons). Could you please let me know what is their ensembl name? (from listFilters(mart)?). thank you! best regards Galina [[alternative HTML version deleted]] _______________________________________________ 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]]
ADD REPLYlink written 9.3 years ago by Glazko, Galina350
Galina, It seems that there is no filter called ensembl_exon_id, the biomaRt team might be better at clarifying this or pointing you to the right filter. A workaround solution would be, ExonWithGene = getBM(c("ensembl_exon_id", ”mgi_description”,”mgi_symbol”), mart = mart) You could then merge the results with ExonWithGene. Again, the biomaRt team might get you a more elegant solution. Kind regards, Julie On 9/9/10 2:15 PM, "Glazko, Galina" <galina_glazko@urmc.rochester.edu> wrote: Julie, yes I tried this but it did not work: > getBM(attributes=c("chromosome_name"),filters="ensembl_exon_id",valu es=c("ENSMUSE00000844234"), mart=mart) Error in getBM(attributes = c("chromosome_name"), filters = "ensembl_exon_id", : Invalid filters(s): ensembl_exon_id Please use the function 'listFilters' to get valid filter names > I do not understand why. best regards Galina ________________________________ From: Zhu, Julie [Julie.Zhu@umassmed.edu] Sent: Thursday, September 09, 2010 2:07 PM To: Glazko, Galina; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] mouse SNPs annotation with ChIPpeakAnno Galina, Since you used Exon as featureType, the feature column is the ensembl_exon_id instead of ensembl_gene ID. Kind regards, Julie On 9/9/10 1:53 PM, "Glazko, Galina" <galina_glazko@urmc.rochester.edu <urlblockederror.aspx=""> > wrote: Dear Vincent and Julie, thank you for the helpful hints! Julie, annotatePeakInBatch works great! But now I have another question: I am trying to annotate these feautures I got back (using Annotation = getAnnotation(mart, featureType="Exon")) and I have this table: space start end width names peak strand feature 1 17 45883787 45883887 101 mm37-17-45883787 ENSMUSE00000844234 mm37-17-45883787 1 ENSMUSE00000844234 2 17 29434504 29434604 101 NES16571232 ENSMUSE00000813877 NES16571232 1 ENSMUSE00000813877 3 17 29428231 29428331 101 NES16571402 ENSMUSE00000421676 NES16571402 1 ENSMUSE00000421676 4 17 31949127 31949227 101 NES15760823 ENSMUSE00000493746 NES15760823 -1 ENSMUSE00000493746 5 17 31948263 31948363 101 NES15760902 ENSMUSE00000493746 NES15760902 -1 ENSMUSE00000493746 6 17 31948318 31948418 101 NES15760903 ENSMUSE00000493746 NES15760903 -1 ENSMUSE00000493746 7 17 29329081 29329181 101 NES16573923 ENSMUSE00000762871 NES16573923 -1 ENSMUSE00000762871 8 17 29328546 29328646 101 NES16573940 ENSMUSE00000762871 NES16573940 -1 ENSMUSE00000762871 9 17 29328568 29328668 101 NES16573943 ENSMUSE00000762871 NES16573943 -1 ENSMUSE00000762871 10 17 29327513 29327613 101 NES16573962 ENSMUSE00000762871 NES16573962 -1 ENSMUSE00000762871 11 17 29327728 29327828 101 NES16573970 ENSMUSE00000762871 NES16573970 -1 ENSMUSE00000762871 12 17 29327208 29327308 101 NES16573987 ENSMUSE00000762871 NES16573987 -1 ENSMUSE00000762871 13 17 29327324 29327424 101 NES16573988 ENSMUSE00000762871 NES16573988 -1 ENSMUSE00000762871 14 17 29326956 29327056 101 NES16573997 ENSMUSE00000762871 NES16573997 -1 ENSMUSE00000762871 15 17 29316818 29316918 101 NES16574121 ENSMUSE00000726199 NES16574121 -1 ENSMUSE00000726199 I thought that these identifiers (e.g. 'ENSMUSE00000844234') are ensembl genes and wanted to get back gene names and descriptions. Apparently I was wrong: if I try e.g. getBM(attributes=c("mgi_description","mgi_symbol"),filters='ensembl_ge ne_id',values=c("ENSMUSE00000844234"), mart=mart) I get nothing back (same with transcripts and exons). Could you please let me know what is their ensembl name? (from listFilters(mart)?). thank you! best regards Galina [[alternative HTML version deleted]]
ADD REPLYlink written 9.3 years ago by Julie Zhu4.1k
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