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]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >