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Question: manhattan plot with Fst values
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Hello all dears, Actually I was going to do a manhattan plot with the package (qqman). I have prepared a .txt file with 3 columns including "CHR", "BP" and "P". when I run my command it says that the column "CHR" not found. I will be so grateful if anybody can help me in this regard. Here is the command which I am using:

manhattan("mydata.txt", chr= "CHR", bp= "BP", p= "P", logp= FALSE, ylim=c(0,1))

and this is the error:

Column CHR not found!

and this is the link for type of file which I have used:

Thank you very much in advance.

ADD COMMENTlink 13 months ago jaafari.omid • 40 • updated 13 months ago RamRS 21k
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Please post your whole code here. How have you imported the data in R?

ADD REPLYlink 13 months ago
prasundutta87
• 330
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I think I found the problem.

This is the command which I was using:

manhattan ("C:/user/omid/desktop/sample.txt", bp= "BP", chr= "CHR", p= "P", logp= FALSE, ylim=c(0,1))

but first I should introduce a variant for my input file I think., Like:

x= read.delim("C:/user/omid/desktop/sample.txt")

and then:

manhattan (x, bp= "BP", chr= "CHR", p= "P", logp= FALSE, ylim=c(0,1))

now it works fortunately.

ADD REPLYlink 13 months ago
jaafari.omid
• 40 •
updated 13 months ago
RamRS
21k
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Right..you need to import your input data in R first before you do anything with it...

ADD REPLYlink 13 months ago
prasundutta87
• 330
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Hello jaafari.omid

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ADD REPLYlink 13 months ago
RamRS
21k

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