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]]
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
>
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
>
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]]
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]]
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]]
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]]
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]]
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
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