MANQQ.R
This app will take a text file with GWAS summary statistics as input and output Manhattan plot and QQ-plot. Run it as an executable from command line to see all the available options.
Usage: ./manqq.R [options]
Options:
-f CHARACTER, --file=CHARACTER
Text file with the columns P, CHROM and POS, it can also be compressed (.gz)
-r CHARACTER, --chromosome=CHARACTER
Column name for the chromosome, [default = CHR]
-b CHARACTER, --basepair=CHARACTER
Column name for the genomic position, [default = BP]
-p CHARACTER, --pvalue=CHARACTER
Column name for the association p-value, [default = P]
-c LOGICAL, --cut=LOGICAL
To speed up plotting, cut out snps with P > 0.05, [default = FALSE]
-m CHARACTER, --manout=CHARACTER
output file name [default = out(.manhattan.png)]
-t NUMERIC, --threshold=NUMERIC
threshold line for suggestive significance [default = 5e-06]
-q CHARACTER, --qqout=CHARACTER
output file name [default = out(qq.png)]
-h, --help
Show this help message and exit