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Error in p values should be at range of (0, 1). #124

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Liny2333 opened this issue May 8, 2024 · 3 comments
Open

Error in p values should be at range of (0, 1). #124

Liny2333 opened this issue May 8, 2024 · 3 comments

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@Liny2333
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Liny2333 commented May 8, 2024

Can you please help me understanding the error thrown by CMplot?
There is my code:
data2<-read.table('newdata_1-6', head=TRUE)
data2<-data2[order(data2[,2]),]
library(CMplot)
CMplot(data2,plot.type="c",
r=0.4,col=c("grey30","grey60"),
chr.labels=paste("Chr",c(1:6),sep=""),
threshold=c(1e-6,1e-4),cir.chr.h=1.5,
amplify=TRUE,threshold.lty=c(1,2),
threshold.col=c("red","blue"),signal.line=1,
signal.col=c("red","green"),
chr.den.col=c("darkgreen","yellow","red"),
bin.size=1e6,outward=FALSE,file="pdf",
dpi=300,file.output=TRUE,verbose=TRUE)
My data have the '0' values and I wonder if Manhattan can't be mapped with a p-value of zero.

@Liny2333
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Liny2333 commented May 8, 2024

1715150444706

@Liny2333
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Liny2333 commented May 8, 2024

And the error is Error in CMplot(data2, plot.type = "c", r = 0.4, col = c("grey30", "grey60"), :
p values should be at range of (0, 1).

@Liny2333
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Liny2333 commented May 8, 2024

I also try to use the other data which without a p-value of zero and i 've got the plot.How can I use data with a value of 0 to draw a circular Manhattan plot?

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