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manhattan plot with Fst values
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2.2 years ago
jaafari.omid • 40
@jaafari.omid42947

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.

SNP software error • 498 views
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Please post your whole code here. How have you imported the data in R?

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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.

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Right..you need to import your input data in R first before you do anything with it...

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Hello jaafari.omid

  • Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
    code_formatting

  • See How to add images to a Biostars post to add your images properly

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