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

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

anikaM
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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Re: Error in plot.window(...) : need finite 'ylim' values

Jim Lemon-4
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 <[hidden email]> 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
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.