manhattan plot with Fst values

Question

[jaafari.omid]

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.

[prasundutta87]

Please post your whole code here. How have you imported the data in R?

[jaafari.omid]

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.

[prasundutta87]

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

[Ram]

Hello jaafari.omid

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