ChIPpeakAnno, getAnnotation question
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Dear Daria, By default, getAnnotation assumes featureType TSS. Currently, the parameter featureType accepts one of the feature types (case sensitive): "TSS","miRNA", "Exon", "5utr", "3utr" or "ExonPlusUtr". For example, 5utr for 5 UTR. You were right that with parameter featureType set to TSS, getAnnotation returns the gene coordinates. If you think it is useful to have transcript coordinates, I will be happy to add featureType transcript. Thanks! Best regards, Julie On 8/25/11 4:00 PM, "Daria Goranskaya" <daria.goranskaya at="" gmail.com=""> wrote: > Dear Julie: > > I'm PhD student in bioinformatics in Karolinska Institutet, Stockholm. > I've been using ChIPpeakAnno for my data and I found something strange > with getting annotation using getAnnotation function. Could you take > a look on the following? > >> library("biomaRt") >> library("ChIPpeakAnno") >> mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl") >> EnsemblAnnotation<-as.data.frame(getAnnotation(mart, >> featureType=c("TSS","miRNA", "Exon", "5utr", "3utr", "ExonPlusUtr"))) >> EnsemblTSS<-as.data.frame(getAnnotation(mart, featureType=c("TSS"))) > > When I tried to get TSS , I got not transcripts, but genes. And the > last two commands gave the same results! That's strange, because in > the first command there should be plenty of other features except TSS. > Also I got an error, when asking for 5UTR. > > How should I use this function to get necessary annotation features? > hank you in advance! > > Best regards, > Daria > > > P.S. Here is the whole R history: > >> library("biomaRt") >> library("ChIPpeakAnno") >> mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl") >> EnsemblAnnotation<-as.data.frame(getAnnotation(mart, >> featureType=c("TSS","miRNA", "Exon", "5utr", "3utr", "ExonPlusUtr"))) >> EnsemblTSS<-as.data.frame(getAnnotation(mart, featureType=c("TSS"))) >> Ensembl5utr<-as.data.frame(getAnnotation(mart, featureType=c("5utr"))) > Warnings: > 1: In getAnnotation(mart, featureType = c("5utr")) : > Following duplicated IDs found, only one of entries of the > duplicated id will be returned! > 2: In getAnnotation(mart, featureType = c("5utr")) : > > ENST00000400678ENST00000400776ENST00000400776ENST00000546775ENST0000 0550740ENS > T00000546775ENST00000550740ENST00000546775ENST00000451927ENST0000040 0890ENST00 > 000550740ENST00000552764ENST00000546832ENST00000549120ENST0000055074 0ENST00000 > 546775ENST00000552764ENST00000546736ENST00000346061ENST00000447903EN ST00000272 > 035ENST00000413237ENST00000447903ENST00000346061ENST00000418749ENST0 0000400681 > ENST00000418749ENST00000346061ENST00000400840ENST00000262316ENST0000 0420545ENS > T00000450643ENST00000454039ENST00000338527ENST00000219431ENST0000043 6333ENST00 > 000397817ENST00000551377ENST00000368372ENST00000314367ENST0000043109 9ENST00000 > 382389ENST00000399951ENST00000323434ENST00000331302ENST00000399951EN ST00000551 > 377ENST00000456528ENST00000521270ENST00000521145ENST00000523418ENST0 0000308811 > ENST00000523162ENST00000522866ENST00000518414ENST00000521270ENST0000 0320552ENS > T00000398612ENST00000325113ENST00000525282ENST00000540150ENST0000034 2593ENST00 > 000399012ENST00000445062ENST00000429181ENST00000399012ENST000004 > [... truncated] >> head(EnsemblAnnotation) > space start end width names strand > 1 1 11869 14412 2544 ENSG00000223972 1 > 2 1 14363 29806 15444 ENSG00000227232 -1 > 3 1 29554 31109 1556 ENSG00000243485 1 > 4 1 30366 30503 138 ENSG00000221311 1 > 5 1 34554 36081 1528 ENSG00000237613 -1 > 6 1 62948 63887 940 ENSG00000240361 1 > > description > 1 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1 > [Source:HGNC Symbol;Acc:37102] > 2 WAS protein family homolog 7 pseudogene > [Source:HGNC Symbol;Acc:38034] > 3 microRNA 1302-10 > [Source:HGNC Symbol;Acc:38233] > 4 microRNA 1302-10 > [Source:HGNC Symbol;Acc:38233] > 5 family with sequence similarity 138, member A > [Source:HGNC Symbol;Acc:32334] > 6 olfactory receptor, family 4, subfamily G, member 11 pseudogene > [Source:HGNC Symbol;Acc:31276] >> head(EnsemblTSS) > space start end width names strand > 1 1 11869 14412 2544 ENSG00000223972 1 > 2 1 14363 29806 15444 ENSG00000227232 -1 > 3 1 29554 31109 1556 ENSG00000243485 1 > 4 1 30366 30503 138 ENSG00000221311 1 > 5 1 34554 36081 1528 ENSG00000237613 -1 > 6 1 62948 63887 940 ENSG00000240361 1 > > description > 1 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1 > [Source:HGNC Symbol;Acc:37102] > 2 WAS protein family homolog 7 pseudogene > [Source:HGNC Symbol;Acc:38034] > 3 microRNA 1302-10 > [Source:HGNC Symbol;Acc:38233] > 4 microRNA 1302-10 > [Source:HGNC Symbol;Acc:38233] > 5 family with sequence similarity 138, member A > [Source:HGNC Symbol;Acc:32334] > 6 olfactory receptor, family 4, subfamily G, member 11 pseudogene > [Source:HGNC Symbol;Acc:31276] >> head(Ensembl5utr) > space start end width names strand > 1 1 35737 36081 345 ENST00000417324 -1 > 2 1 367640 367658 19 ENST00000426406 1 > 3 1 622035 622053 19 ENST00000332831 -1 > 4 1 721320 721405 86 ENST00000358533 1 > 5 1 860260 860328 69 ENST00000420190 1 > 6 1 860530 860569 40 ENST00000437963 1 > > description > 1 family with sequence similarity 138, member A [Source:HGNC > Symbol;Acc:32334] > 2 olfactory receptor, family 4, subfamily F, member 29 [Source:HGNC > Symbol;Acc:31275] > 3 olfactory receptor, family 4, subfamily F, member 16 [Source:HGNC > Symbol;Acc:15079] > 4 Transmembrane protein FLJ78588 > [Source:UniProtKB/Swiss-Prot;Acc:A6NHI5] > 5 sterile alpha motif domain containing 11 [Source:HGNC > Symbol;Acc:28706] > 6 sterile alpha motif domain containing 11 [Source:HGNC > Symbol;Acc:28706] > > > >
Annotation microRNA ChIPpeakAnno Annotation microRNA ChIPpeakAnno • 1.1k views
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
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Daria, The warnings you experienced with 5utr has been fixed and transcript has been added as an option for featureType. Please download the 2.0.2 version. Thanks for your input! Best regards, Julie On 8/29/11 10:56 AM, "Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: > Dear Daria, > > By default, getAnnotation assumes featureType TSS. Currently, the parameter > featureType accepts one of the feature types (case sensitive): > "TSS","miRNA", "Exon", "5utr", "3utr" or "ExonPlusUtr". For example, 5utr > for 5 UTR. > > You were right that with parameter featureType set to TSS, getAnnotation > returns the gene coordinates. If you think it is useful to have transcript > coordinates, I will be happy to add featureType transcript. Thanks! > > Best regards, > > Julie > > > > > > On 8/25/11 4:00 PM, "Daria Goranskaya" <daria.goranskaya at="" gmail.com=""> wrote: > >> Dear Julie: >> >> I'm PhD student in bioinformatics in Karolinska Institutet, Stockholm. >> I've been using ChIPpeakAnno for my data and I found something strange >> with getting annotation using getAnnotation function. Could you take >> a look on the following? >> >>> library("biomaRt") >>> library("ChIPpeakAnno") >>> mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl") >>> EnsemblAnnotation<-as.data.frame(getAnnotation(mart, >>> featureType=c("TSS","miRNA", "Exon", "5utr", "3utr", "ExonPlusUtr"))) >>> EnsemblTSS<-as.data.frame(getAnnotation(mart, featureType=c("TSS"))) >> >> When I tried to get TSS , I got not transcripts, but genes. And the >> last two commands gave the same results! That's strange, because in >> the first command there should be plenty of other features except TSS. >> Also I got an error, when asking for 5UTR. >> >> How should I use this function to get necessary annotation features? >> hank you in advance! >> >> Best regards, >> Daria >> >> >> P.S. Here is the whole R history: >> >>> library("biomaRt") >>> library("ChIPpeakAnno") >>> mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl") >>> EnsemblAnnotation<-as.data.frame(getAnnotation(mart, >>> featureType=c("TSS","miRNA", "Exon", "5utr", "3utr", "ExonPlusUtr"))) >>> EnsemblTSS<-as.data.frame(getAnnotation(mart, featureType=c("TSS"))) >>> Ensembl5utr<-as.data.frame(getAnnotation(mart, featureType=c("5utr"))) >> Warnings: >> 1: In getAnnotation(mart, featureType = c("5utr")) : >> Following duplicated IDs found, only one of entries of the >> duplicated id will be returned! >> 2: In getAnnotation(mart, featureType = c("5utr")) : >> >> ENST00000400678ENST00000400776ENST00000400776ENST00000546775ENST000005 50740EN>> S >> T00000546775ENST00000550740ENST00000546775ENST00000451927ENST000004008 90ENST0>> 0 >> 000550740ENST00000552764ENST00000546832ENST00000549120ENST00000550740E NST0000>> 0 >> 546775ENST00000552764ENST00000546736ENST00000346061ENST00000447903ENST 0000027>> 2 >> 035ENST00000413237ENST00000447903ENST00000346061ENST00000418749ENST000 0040068>> 1 >> ENST00000418749ENST00000346061ENST00000400840ENST00000262316ENST000004 20545EN>> S >> T00000450643ENST00000454039ENST00000338527ENST00000219431ENST000004363 33ENST0>> 0 >> 000397817ENST00000551377ENST00000368372ENST00000314367ENST00000431099E NST0000>> 0 >> 382389ENST00000399951ENST00000323434ENST00000331302ENST00000399951ENST 0000055>> 1 >> 377ENST00000456528ENST00000521270ENST00000521145ENST00000523418ENST000 0030881>> 1 >> ENST00000523162ENST00000522866ENST00000518414ENST00000521270ENST000003 20552EN>> S >> T00000398612ENST00000325113ENST00000525282ENST00000540150ENST000003425 93ENST0>> 0 >> 000399012ENST00000445062ENST00000429181ENST00000399012ENST000004 >> [... truncated] >>> head(EnsemblAnnotation) >> space start end width names strand >> 1 1 11869 14412 2544 ENSG00000223972 1 >> 2 1 14363 29806 15444 ENSG00000227232 -1 >> 3 1 29554 31109 1556 ENSG00000243485 1 >> 4 1 30366 30503 138 ENSG00000221311 1 >> 5 1 34554 36081 1528 ENSG00000237613 -1 >> 6 1 62948 63887 940 ENSG00000240361 1 >> >> description >> 1 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1 >> [Source:HGNC Symbol;Acc:37102] >> 2 WAS protein family homolog 7 pseudogene >> [Source:HGNC Symbol;Acc:38034] >> 3 microRNA 1302-10 >> [Source:HGNC Symbol;Acc:38233] >> 4 microRNA 1302-10 >> [Source:HGNC Symbol;Acc:38233] >> 5 family with sequence similarity 138, member A >> [Source:HGNC Symbol;Acc:32334] >> 6 olfactory receptor, family 4, subfamily G, member 11 pseudogene >> [Source:HGNC Symbol;Acc:31276] >>> head(EnsemblTSS) >> space start end width names strand >> 1 1 11869 14412 2544 ENSG00000223972 1 >> 2 1 14363 29806 15444 ENSG00000227232 -1 >> 3 1 29554 31109 1556 ENSG00000243485 1 >> 4 1 30366 30503 138 ENSG00000221311 1 >> 5 1 34554 36081 1528 ENSG00000237613 -1 >> 6 1 62948 63887 940 ENSG00000240361 1 >> >> description >> 1 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1 >> [Source:HGNC Symbol;Acc:37102] >> 2 WAS protein family homolog 7 pseudogene >> [Source:HGNC Symbol;Acc:38034] >> 3 microRNA 1302-10 >> [Source:HGNC Symbol;Acc:38233] >> 4 microRNA 1302-10 >> [Source:HGNC Symbol;Acc:38233] >> 5 family with sequence similarity 138, member A >> [Source:HGNC Symbol;Acc:32334] >> 6 olfactory receptor, family 4, subfamily G, member 11 pseudogene >> [Source:HGNC Symbol;Acc:31276] >>> head(Ensembl5utr) >> space start end width names strand >> 1 1 35737 36081 345 ENST00000417324 -1 >> 2 1 367640 367658 19 ENST00000426406 1 >> 3 1 622035 622053 19 ENST00000332831 -1 >> 4 1 721320 721405 86 ENST00000358533 1 >> 5 1 860260 860328 69 ENST00000420190 1 >> 6 1 860530 860569 40 ENST00000437963 1 >> >> description >> 1 family with sequence similarity 138, member A [Source:HGNC >> Symbol;Acc:32334] >> 2 olfactory receptor, family 4, subfamily F, member 29 [Source:HGNC >> Symbol;Acc:31275] >> 3 olfactory receptor, family 4, subfamily F, member 16 [Source:HGNC >> Symbol;Acc:15079] >> 4 Transmembrane protein FLJ78588 >> [Source:UniProtKB/Swiss-Prot;Acc:A6NHI5] >> 5 sterile alpha motif domain containing 11 [Source:HGNC >> Symbol;Acc:28706] >> 6 sterile alpha motif domain containing 11 [Source:HGNC >> Symbol;Acc:28706] >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Julie Zhu ★ 4.3k
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Dear Daria, You could download the most recent version from the repository using svn. svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAn no/ Alternatively, you could download ChIPpeakAnno_2.0.3.tar.gz at http://www.bioconductor.org/packages/2.9/bioc/html/ChIPpeakAnno.html (It will take a couple of days for the version 2.0.3 to appear yet). Best regards, Julie On 8/29/11 1:29 PM, "Daria Goranskaya" <daria.goranskaya at="" gmail.com=""> wrote: > Dear Julie: > > Thank you! Where can I download new version? On bionconductor site > there is still the old one. > > Best regards, > Daria > > On Mon, Aug 29, 2011 at 6:46 PM, Zhu, Lihua (Julie) > <julie.zhu at="" umassmed.edu=""> wrote: >> Daria, >> >> The warnings you experienced with 5utr has been fixed and transcript has >> been added as an option for featureType. Please download the 2.0.2 version. >> >> Thanks for your input! >> >> Best regards, >> >> Julie >> >> >> On 8/29/11 10:56 AM, "Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: >> >>> Dear Daria, >>> >>> By default, getAnnotation assumes featureType TSS. Currently, the parameter >>> featureType accepts one of the feature types (case sensitive): >>> "TSS","miRNA", "Exon", "5utr", "3utr" or "ExonPlusUtr". For example, 5utr >>> for 5 UTR. >>> >>> You were right that with parameter featureType set to TSS, getAnnotation >>> returns the gene coordinates. If you think it is useful to have transcript >>> coordinates, I will be happy to add featureType transcript. Thanks! >>> >>> Best regards, >>> >>> Julie >>> >>> >>> >>> >>> > > ******************************** > Dariya Goranskaya > PhD student > Unit of Computational Medicine, > Department of Medicine, > Karolinska Institutet > Stockholm, Sweden > email: dariya.goranskaya at ki.se > ? ? ? ? ?daria.goranskaya at gmail.com > Office Number: +46 8 517 708 69 > ********************************
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