[BioC] snapCGH genomePlot chrominfo

[Sean Davis]

On Fri, Apr 23, 2010 at 8:44 AM, Chris Fenton <chrisf at fagmed.uit.no> wrote:
> function (input, array = 1, naut = 22, Y = FALSE, X = FALSE,
>    main = NA, status, values, pch, cex, col, chrominfo = chrominfo.Mb,
>    ylim = c(-2, 2), ylb = "Log2Ratio", chrom.to.plot = NA, xlim = c(0,
>        NA), ...)
>
>
> ma2                <- processCGH(ma1)
> seginfo.dna        <- runDNAcopy(ma2)
> genomePlot(seginfo.dna.merged, array=1, chrom.to.plot=8,
> chrominfo=1000)
>
> fails.
>
> Error in attr(status, status.attr[ii]) : 'which' must be of mode
> character
>
> I can remove the status lines from the code but I am still getting an
> error on chrominfo
> What is expected in the parameter ?

It isn't entirely clear from the help for genomePlot, but a little
digging turns up:

help(chrominfo.Mb)

This help page describes the format for the data frame that is meant
to be passed into the chrominfo parameter.

Sean