Input file of NGS data for Pathview
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amoltej ▴ 10
@amoltej-7192
Last seen 5.2 years ago
Australia

Hi, 

I have RNA seq data for different tissues of non-model insect. I want to visualize the pathway connection between these two tissues. for that I am planning to use pathview. But there is no clear cut example of input data set. I have already mapped my transcripts with drosophilla KEGG database. and I have got list of genes and pathways that are represented by the dataset. it has log fold change data as well. But I am not able to figure out which data I should provide to the pathview?

can someone please tell me what the input data should look like? and if any further information to get maximum out of pathview?

Thank you in advance

Amol

rnaseq pathview data visualization • 2.0k views
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Luo Weijun ★ 1.6k
@luo-weijun-1783
Last seen 3 months ago
United States
Pathview accepts either a matrix or vector as input gene data. It can be numeric (like log2 fold change or absolute expression levels) or gene IDs, depends on what you want to visualize. I would suggest you to go through the documentation of the pathview function, which shows all the technical details as to use it. In R, you can do: library(pathview) ?pathview In addition, you can follow the tutorial with specific examples: http://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf there is also a tutorial on complete RNA-Seq pathway analysis workflow in gage package: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf -------------------------------------------- On Mon, 10/26/15, amoltej [bioc] <noreply@bioconductor.org> wrote: Subject: [bioc] Input file of NGS data for Pathview To: luo_weijun@yahoo.com Date: Monday, October 26, 2015, 8:48 PM Activity on a post you are following on support.bioconductor.org User amoltej wrote Question: Input file of NGS data for Pathview: Hi,� I have RNA seq data for different tissues of non-model insect. I want to visualize the pathway connection between these two tissues. for that I am planning to use pathview. But there is no clear cut example of input data set. I have already mapped my transcripts with drosophilla KEGG database. and I have got list of genes and pathways that are represented by the dataset. it has log fold change data as well. But I am not able to figure out which data I should provide to the pathview? can someone please tell me what the input data should look like? and if any further information to get maximum out of pathview? Thank you in advance Amol Post tags: rnaseq, pathview, data visualization You may reply via email or visit Input file of NGS data for Pathview
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