Plotting Gwas Meta-Analysis Output From Metal

Question

[hmbarek]

Hi all, Is there any tools to quickly plot the manhattan plot and QQ plot for summary statistics of METAL output. here an idea about the outputs of METAL This file contains a short description of the columns in the meta-analysis summary file, named 'MA.tbl'

# Marker    - this is the marker name
# Allele1   - the first allele for this marker in the first file where it occurs
# Allele2   - the second allele for this marker in the first file where it occurs
# Freq1       - weighted average of frequency for allele 1 across all studies
# FreqSE      - corresponding standard error for allele frequency estimate
# MinFreq     - minimum frequency for allele 1 across all studies
# MaxFreq     - maximum frequency for allele 1 across all studies
# Weight    - the sum of the individual study weights (typically, N) for this marker
# Z-score   - the combined z-statistic for this marker
# P-value   - meta-analysis p-value
# Direction - summary of effect direction for each study, with one '+' or '-' per study

thank you

regards

Answer 1

[Philipp Bayer]

Here's a simple R-script to make a QQ-plot, it only needs the p-values: https://www.broadinstitute.org/files/shared/diabetes/scandinavs/qqplot.R (source)

For the Manhattan plot you need to know the positions of SNPs (and the chromosome number if there are several), and your file doesn't seem to have it. Do you have the positions somewhere else? Here's an example for a Manhattan plot and QQ plot in R once you got the positions: http://gettinggeneticsdone.blogspot.com.au/2011/04/annotated-manhattan-plots-and-qq-plots.html

Answer 2

[Anthony]

Simple R code:

pval <- runif(250)
theory <- ppoints(length(pval))
qqplot(theory, pval, xlim=c(0,1), ylim=c(0,1))
abline(a=0,b=1)

pval: the vector of p-value theory: the theoretical distribution

Feel free to take the -log() if you wish.