OmicCircos mapping data file.
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abdul rawoof ▴ 60
@abdul-rawoof-5869
Last seen 2.7 years ago
United States

Hi all,

Could anyone can help me to create mapping data file format used in OmicCircos.
I want to make "mapping data file" for my expression data. I have a set of genes for which I got chromosome start and chromosome end position.
As mentioned in OmicCircos the mapping data file have chromosome position ( "Po") , I tried to get it for my set of genes but couldn't get it.

From where I can get this information.

Thanks

omiccircos • 1.0k views
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@james-w-macdonald-5106
Last seen 18 hours ago
United States

Looking at the vignette for OmicCircos, there is an example mapping file on page 4, and the vignette states that the second column ('Po' column) is the position. It's not clear what 'position' means in this context, so let's do an experiment!

The first gene is ISG15. I don't see the build, but it is TCGA data, so I assume it is a bit old, probably hg18. So I went to UCSC's browser, punched in that gene name and got:

ISG15 (uc001acj.2) at chr1:938710-939782

as the first hit for the hg18 build. But the value in the vignette is 939245.5, which is somewhere between the start and end of that gene. So I used my trusty slide rule to calculate the mean of the start/end value that I get from UCSC, and I get 939246, which is close enough for government work. So I assume that the position is the middle of the gene, which you can easily compute if you have the start/end values.

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Thanks, It's really helpful for me...I also thought in the same way but I was using hg19 built thats why I was not getting correct position value.

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@hu-ying-nihnci-e-6375
Last seen 5.5 years ago
United States

OmicCircos was updated http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html

Please let me know if you have any questions.

Thanks

Ying

yhu@mail.nih.gov