Biostar Beta. Not for public use.
Question: manhattan plot with Fst values
0
Entering edit mode

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 15 months ago jaafari.omid • 40 • updated 15 months ago RamRS 21k
Entering edit mode
0

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

ADD REPLYlink 15 months ago
prasundutta87
• 330
Entering edit mode
0

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 15 months ago
jaafari.omid
• 40
• updated 15 months ago
RamRS
21k
Entering edit mode
0

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

ADD REPLYlink 15 months ago
prasundutta87
• 330
Entering edit mode
0

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

  • Always add relevant tags, and invest some effort before you create a post.

  • Do not post screenshots of text, paste the text directly instead.

ADD REPLYlink 15 months ago
RamRS
21k

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.0