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stephenturner / qqman

An R package for creating Q-Q and manhattan plots from GWAS results
http://cran.r-project.org/web/packages/qqman/
GNU General Public License v3.0
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Column CHR not found! #62

Closed geneticsmcgill closed 6 years ago

geneticsmcgill commented 6 years ago

Hello,

I've been trying to plot some sample data with the manhattan() function and it keeps saying this:

library(qqman) manhattan(ETtrait1polygenicv4) Error in manhattan(ETtrait1polygenicv4) : Column CHR not found!

I was wondering if you had any advice on how to proceed? Thank you so much for the wonderful program. I've attached the dataset as well. :) ETtrait1polygenicv4.xlsx

stephenturner commented 6 years ago

Please upload a text file or paste something to https://gist.github.com/. The file you uploaded doesn't appear to be a valid excel file.

calpan commented 6 years ago

The posted file (which opens in Excel 2016) has column names that are lower-case where qqman expects upper-case names. Once these are changed to upper-case, the file works fine. Alternatively, the chr, bp, p, and snp options can be used in the manhattan() call, as follows:

ex_data <- readxl::read_excel("ETtrait1polygenicv4.xlsx")
manhattan(ex_data, snp = "snp", chr = "chr", bp = "bp", p = "p")
satish1907 commented 3 years ago

SATAlLSNP1.xlsx The same problem with me also. It always shows manhattan(SATAlLSNP1) : Column CHR not found!

satish1907 commented 3 years ago

SATAlLSNP1.xlsx The same problem with me also. It always shows manhattan(SATAlLSNP1) : Column CHR not found!

Kindly help me in plotting this