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Question: ChIPpeakAnno query
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gravatar for Julie Zhu
4.2 years ago by
Julie Zhu3.6k
United States
Julie Zhu3.6k wrote:
Luke, You need to have chromosome coordinates for the genes. One option is to read the annotation into R using read.table or read.csv, then convert it to RangedData. The other option is to save your gene annotation file as BED format, then use the following command to convert your BED file to the annotation similar to TSS.human.NCBI36. yourAnnotaion = BED2RangedData(read.table(“yourAnnotation.BED”, sep=”\t”)) Here is the code to annotate your peaks with your annotation. AnnotatedPeak = annotatePeakInBatch(“yourPeakInRangedData”, yourAnnotation) For details on how to use ChIPpeakAnno, please see http://www.biocondu ctor.org/packages/2.11/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAn no.pdf http://www.biomedcentral.com/1471-2105/11/237 Please cc <bioconductor@r-project.org>. Thanks! Best regards, Julie On 3/19/13 10:08 PM, "Luke Selth" <luke.selth@adelaide.edu.au> wrote: Hi Dr Zhu, I’ve just started using ChIPpeakAnno – it’s a great tool. I’ve had no problems annotating my ChIP peaks with TSS (TSS.human.NCBI36) and other genomic features. Now I’m trying to annotate my ChIP peaks with just a list of regulated genes that were generated by Affy microarray. I want to determine if my peaks are closer to these genes than the rest of the genome. I have converted the gene list to Ensembl gene IDs and extracted the TSS data using BiomaRt. However, I don’t know what to do next! I would like to convert the TSS data from my gene list into something like the “TSS.human.NCBI36” object that ChIPpeakAnno can interpret – any idea how to do this? Cheers, Luke ------ Luke Selth, PhD US Prostate Cancer Foundation Young Investigator Dame Roma Mitchell Cancer Research Laboratories University of Adelaide & Hanson Institute PO Box 14, Rundle Mall Adelaide, SA 5000 AUSTRALIA Phone: (+618) 8222 3618 Fax: (+618) 8222 3217 Email: luke.selth@adelaide.edu.au [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.2 years ago by Luke Selth10 • written 4.2 years ago by Julie Zhu3.6k
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gravatar for Luke Selth
4.2 years ago by
Luke Selth10
Luke Selth10 wrote:
Hi Julie, Many thanks for the prompt reply. I have been able to annotate the peaks with the chromosome coordinates of the regulated genes. However, the problem with loading my gene list in as a bed file and then converting it to Ranged Data is that it lacks strand information. This means that the annotatePeakInBatch command can't tell whether the first coordinate is the start or the stop (for -1 genes, the second coordinate is the start) and thus the distanceToFeature output does not always correspond to the TSS. Regardless, thanks for your help - I'm sure I can sort out a quick work around in Excel, but I thought I might be able to do it all in ChIPpeakAnno. Cheers, Luke From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu] Sent: Wednesday, 20 March 2013 1:08 PM To: Luke Selth Cc: <bioconductor@r-project.org> Subject: Re: ChIPpeakAnno query Luke, You need to have chromosome coordinates for the genes. One option is to read the annotation into R using read.table or read.csv, then convert it to RangedData. The other option is to save your gene annotation file as BED format, then use the following command to convert your BED file to the annotation similar to TSS.human.NCBI36. yourAnnotaion = BED2RangedData(read.table("yourAnnotation.BED", sep="\t")) Here is the code to annotate your peaks with your annotation. AnnotatedPeak = annotatePeakInBatch("yourPeakInRangedData", yourAnnotation) For details on how to use ChIPpeakAnno, please see http://www.biocondu ctor.org/packages/2.11/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAn no.pdf http://www.biomedcentral.com/1471-2105/11/237 Please cc <bioconductor@r-project.org>. Thanks! Best regards, Julie On 3/19/13 10:08 PM, "Luke Selth" <luke.selth@adelaide.edu.au> wrote: Hi Dr Zhu, I've just started using ChIPpeakAnno - it's a great tool. I've had no problems annotating my ChIP peaks with TSS (TSS.human.NCBI36) and other genomic features. Now I'm trying to annotate my ChIP peaks with just a list of regulated genes that were generated by Affy microarray. I want to determine if my peaks are closer to these genes than the rest of the genome. I have converted the gene list to Ensembl gene IDs and extracted the TSS data using BiomaRt. However, I don't know what to do next! I would like to convert the TSS data from my gene list into something like the "TSS.human.NCBI36" object that ChIPpeakAnno can interpret - any idea how to do this? Cheers, Luke ------ Luke Selth, PhD US Prostate Cancer Foundation Young Investigator Dame Roma Mitchell Cancer Research Laboratories University of Adelaide & Hanson Institute PO Box 14, Rundle Mall Adelaide, SA 5000 AUSTRALIA Phone: (+618) 8222 3618 Fax: (+618) 8222 3217 Email: luke.selth@adelaide.edu.au [[alternative HTML version deleted]]
ADD COMMENTlink written 4.2 years ago by Luke Selth10
Luke, Great! Thanks for letting me know! You can add strand information in the RangedData as space . Alternatively, you could use getAnnotation function in ChIPpeakAnno to retrieve the TSS information. If you are interested in connecting ChIP data and microarray data, I would recommend you try out our GeneNetworkBuilder package. Best regards, Julie On 3/19/13 11:30 PM, "Luke Selth" <luke.selth@adelaide.edu.au> wrote: Hi Julie, Many thanks for the prompt reply. I have been able to annotate the peaks with the chromosome coordinates of the regulated genes. However, the problem with loading my gene list in as a bed file and then converting it to Ranged Data is that it lacks strand information. This means that the annotatePeakInBatch command can’t tell whether the first coordinate is the start or the stop (for -1 genes, the second coordinate is the start) and thus the distanceToFeature output does not always correspond to the TSS. Regardless, thanks for your help – I’m sure I can sort out a quick work around in Excel, but I thought I might be able to do it all in ChIPpeakAnno. Cheers, Luke From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu] Sent: Wednesday, 20 March 2013 1:08 PM To: Luke Selth Cc: <bioconductor@r-project.org> Subject: Re: ChIPpeakAnno query Luke, You need to have chromosome coordinates for the genes. One option is to read the annotation into R using read.table or read.csv, then convert it to RangedData. The other option is to save your gene annotation file as BED format, then use the following command to convert your BED file to the annotation similar to TSS.human.NCBI36. yourAnnotaion = BED2RangedData(read.table(“yourAnnotation.BED”, sep=”\t”)) Here is the code to annotate your peaks with your annotation. AnnotatedPeak = annotatePeakInBatch(“yourPeakInRangedData”, yourAnnotation) For details on how to use ChIPpeakAnno, please see http://www.biocondu ctor.org/packages/2.11/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAn no.pdf http://www.biomedcentral.com/1471-2105/11/237 Please cc <bioconductor@r-project.org>. Thanks! Best regards, Julie On 3/19/13 10:08 PM, "Luke Selth" <luke.selth@adelaide.edu.au> wrote: Hi Dr Zhu, I’ve just started using ChIPpeakAnno – it’s a great tool. I’ve had no problems annotating my ChIP peaks with TSS (TSS.human.NCBI36) and other genomic features. Now I’m trying to annotate my ChIP peaks with just a list of regulated genes that were generated by Affy microarray. I want to determine if my peaks are closer to these genes than the rest of the genome. I have converted the gene list to Ensembl gene IDs and extracted the TSS data using BiomaRt. However, I don’t know what to do next! I would like to convert the TSS data from my gene list into something like the “TSS.human.NCBI36” object that ChIPpeakAnno can interpret – any idea how to do this? Cheers, Luke ------ Luke Selth, PhD US Prostate Cancer Foundation Young Investigator Dame Roma Mitchell Cancer Research Laboratories University of Adelaide & Hanson Institute PO Box 14, Rundle Mall Adelaide, SA 5000 AUSTRALIA Phone: (+618) 8222 3618 Fax: (+618) 8222 3217 Email: luke.selth@adelaide.edu.au [[alternative HTML version deleted]]
ADD REPLYlink written 4.2 years ago by Julie Zhu3.6k
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