[BioC] Plot SNP -log10 pvalues vs chromosomal position

Vincent Carey stvjc at channing.harvard.edu
Fri Oct 9 22:27:49 CEST 2009

As such, this question is not really about Bioconductor but about
plotting data with R.  The GGtools package has examples of such plots,
but it is primarily concerned with the calculation of the p-values.
You might be able to read your file into R using

tab = read.delim([myfile], sep=" ", h=TRUE)

where you put a valid file reference for [myfile] then

with(tab, plot(x=Position, y=-log10(p.value)))

could work ... note that "p-value" is a nonstandard variable name
and would require some special handling; with the commands I have
given, the hyphen would be magically converted to a dot which is
syntactically OK.

To render such information in genomic context, it can be interesting
to push such data to
the genome browser.  rtracklayer can assist with that but if you are
just working with files and are not principally concerned with R,
there are many other possible approaches for this task.

On Fri, Oct 9, 2009 at 4:12 PM, Paul Evans <p.evans48 at yahoo.com> wrote:
> Hi,
> I wanted to plot the -log10 p-values of SNPs vs their chromosomal positions. I have an input file which looks like:
> Chr Ref Position p-value
> 1 rs100045 456789 0.00005
> 3 rs12345 23456 0.00004
> .
> .
> .
> Which bioconductor package would be best for this? I looked at GenABEL and snp.plotter, but both of these seem to require more inputs than the ones I have.
> thanks!
>        [[alternative HTML version deleted]]
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