Error in manhattan(results) : P column should be numeric.

[cjfiscus]

Hi there.

Using qqman package from this link: http://www.r-bloggers.com/qqman-an-r-package-for-creating-q-q-and-manhattan-plots-from-gwas-results/

I formatted my data in format that worked with older version of qqman, substituting NA for missing values. Upon trying to make a manhattan plot I receive the following error:

Error in manhattan(results) : P column should be numeric.

Does qqman no longer deal with missing data?

[stephenturner]

Hm, it should still work.

> gwasResults$P[2] <- NA
> head(gwasResults)
  SNP CHR BP         P
1 rs1   1  1 0.9148060
2 rs2   1  2        NA
3 rs3   1  3 0.2861395
4 rs4   1  4 0.8304476
5 rs5   1  5 0.6417455
6 rs6   1  6 0.5190959
> 
> # works for me
> qq(gwasResults$P)

If you run qq without the parentheses it will print out what the function does. You'll notice the function stops if the p-value vector is not numeric. A numeric vector with NA values is still considered numeric.

> x <- c(1,2,3)
> is.numeric(x)
[1] TRUE
> x <- c(1,NA,3)
> is.numeric(x)
[1] TRUE

Not sure what's going on. Can you put some of your data on https://gist.github.com/?

[cjfiscus]

I was able to figure out how to fix the issue.

https://gist.github.com/cjfiscus/d0f2c883bc1caab0583a

Thank you for your help and for creating such an invaluable tool!

[stephenturner]

Glad you were able to fix your problem, and thanks for the kind words!