solarius (version 0.2.3)

plotManh: Plot the association results

Description

Two Manhattan and quantile-quantile (QQ) plots are standard to explore the results from association studies.

Usage

plotManh(A, alpha = 0.05, main, ...)
plotQQ(A, df = 1, main, ...)

Arguments

A

An object of class solarAssoc.

alpha

A numeric value from 0 to 1, the p-value cut-off for Bonferroni multiple-test correction. The default value is 0.05.

main

A character string, main argument (title) to a plot function. If the argument is missing, the title contains information about the model formula and the number of SNPs used for plotting.

...

additional argument to a plot function.

df

An integer value, the degree of freedom. The default value is 1.

Details

plotManh function produces the Manhattan plot based on qqman package. The two red and blue lines, default in the original manhattan function of qqman package, are preserved. An additional black dashed line is added, that depicts the significance level according to Bonferroni multiple-test correction with alpha argument.

plotQQ function produces the QQ plot based on the same qqman package.

See Also

solarAssocClass

Examples

data(dat50)

assoc <- solarAssoc(trait ~ 1, phenodata,
 snpdata = genodata, snpmap = snpdata, kinship = kin)

plotManh(assoc) # equivalent to plot(assoc)

plotQQ(assoc) # equivalent to plot(assoc, "qq")