Question: Manhattan plot of meta-analysis output from the software meta
1
gravatar for ZB
7 weeks ago by
ZB10
CNAM, France
ZB10 wrote:

I am using imputed chromosomes obtained from Michigan server and then association analysis was done by the software "Meta" from this site: https://mathgen.stats.ox.ac.uk/genetics_software/meta/meta.html

I am using it for meta-analysis because it takes input of SNPtest , which I have used for association analysis. Is there any package or R script to plot manhattan plot from the output of software "Meta"

The out put is like this

chr rsid pos allele_A allele_B P_value coded_af beta se Q P_heterogeneity I2 cohort_1_p cohort_1_beta cohort_1_se cohort_1_info cohort_1_n cohort_2_p cohort_2_beta cohort_2_se cohort_2_info cohort_2_n cohort_3_p cohort_3_beta cohort_3_se cohort_3_info cohort_3_n cohort_4_p cohort_4_beta cohort_4_se cohort_4_info cohort_4_n 
1 1:99295098 1099295098 C A 1.98592e-21 0.00620979 8.40219 0.883905 158.077 4.72197e-35 98.7348 -1 -1 -1 0.317603 
1 1:156921889 1156921889 C T 1.92164e-17 0.0167606 4.14134 0.487306 187.835 1.63024e-41 98.9352 -1 -1 -1 0.308416 
1 1:62263312 1062263312 G A 9.30988e-15 0.00621862 4.39527 0.567253 61.622 4.15868e-14 96.7544 -1 -1 -1 0.320005 
1 1:62214229 1062214229 T A 8.06373e-14 0.00852426 4.04212 0.541166 31.2191 1.66285e-07 93.5937 -1 -1 -1 0.342891 
1 1:247967801 1247967801 G A 3.65778e-13 0.00670116 5.79855 0.797857 27.289 1.18648e-06 92.6711 -1 -1 -1 0.318997 
1 1:52180681 1052180681 T C 1.35948e-12 0.00586743 3.77017 0.531901 14.0097 0.000907481 85.7242 -1 -1 -1 0.718862

I have separate file for each chromosome because Michigan server gives separate files for each chromosome. I need help to combine chromosome files and plot Manhattan as well as QQ plot to make sense of the output. I found one for METAL software at this link https://angus.readthedocs.io/en/2017/meta_GWAS.html#visualize-meta-analysis-results but not for meta.

Your help is appreciated. Thank you

ADD COMMENTlink modified 7 weeks ago by zx87546.7k • written 7 weeks ago by ZB10

Combine all files into one, see "How to read multiple files into R", then read about R qqman package for QQ and Manhattan plots.

ADD REPLYlink written 7 weeks ago by zx87546.7k
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