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Question: Regarding Gviz package
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gravatar for shrutiaggarwal9968
6 months ago by
shrutiaggarwal99680 wrote:

Hi

 

I wanted to know how can I upload the position file in gviz to get the annotation track. My file contains only the single column of positions without any start and end position or any other information. Please help!!!!

ADD COMMENTlink modified 6 months ago by James W. MacDonald45k • written 6 months ago by shrutiaggarwal99680

You cannot define a genomic position without the chromosome, start and end positions. Things like SNPs can be defined by just the chromosome and start position since they are only one base and the end is thus inferred. The same is true for CpG positions, but otherwise you need to know either the end position or the width.

If you were more descriptive, telling us what you want to do and giving an example of the data you have in hand, then people might be able to help you.

ADD REPLYlink written 6 months ago by James W. MacDonald45k

Thank you for your help!!!!!

Can you please help me that how can I convert my excel file to bed file?

ADD REPLYlink written 6 months ago by shrutiaggarwal99680

I'd recommend for you to read up a bit on how to import Excel or tab delimited files into R, and also on the way Bioconductor handles genomic ranges. Gviz is very flexible in terms of inputs. You can provide a data.frame, a GRanges object, paths to various file formats or even populate the necessary fields from numeric or character vectors in the constructor function. This is all documented in much detail with tons of examples in the package vignette and also in the constructor man page:

? AnotationTrack

Florian

ADD REPLYlink written 6 months ago by florian.hahne@novartis.com1.5k
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