[R] Error in plot.window(...) : need finite 'ylim' values

[Jim Lemon]

Hi Ana,
I don't have the qqman package, but is your "P" column in
"M3.assoc.logistic.C" numeric or has it been read in as a factor?

Jim

On Thu, Jun 11, 2020 at 4:13 AM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> Hello,
>
> I do have a file like this:
> head M3.assoc.logistic.C
> CHR SNP BP P
> 1 1:785989:T:C 785989 0.4544
> 1 1:785989:T:C 785989 0.689
> 1 1:1130727:A:C 1130727 0.05068
> 1 1:1130727:A:C 1130727 0.07381
> 1 1:1156131:T:C 1156131 0.6008
> 1 1:1156131:T:C 1156131 0.8685
> ...
>
> And I don't have any "NA" or "inf" values in it
>
> and I am plotting it in R via:
>
> library(qqman)
> results_log <- read.table("M3.assoc.logistic.C", head=TRUE)
> jpeg("Logistic_manhattan_retinopathy_M3.jpeg")
> manhattan(results_log,chr="CHR",bp="BP",p="P",snp="SNP", main =
> "Manhattan plot: logistic")
> dev.off()
>
> but I am getting:
>
> Error in plot.window(...) : need finite 'ylim' values
> Calls: manhattan ... do.call -> plot -> plot.default -> localWindow ->
> plot.window
> Execution halted
>
> Please advise,
>
> Thanks
> Ana
>
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