stratified_qqplot.Rd
Stratified Q-Q plot.
stratified_qqplot( data_frame, prin_value_label, cond_value_label = NULL, thresholds = c(1, 0.1, 0.01, 0.001, 1e-04) )
data_frame |
|
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prin_value_label | label of principal p-value column in |
cond_value_label | label of conditional trait column in |
thresholds | threshold values to define strata |
ggplot object
Can be used to investigate the relationship between p and q
Note that this function does not do the heavy lifting of styling the plot's aesthetics.
# In this example, we generate some p-values (representing GWAS p-values) # and some arbitrary auxiliary data values (e.g. representing GWAS p-values for a related trait). # We use the stratified_qqplot() function to examine the relationship between p and q # generate p set.seed(1) n <- 1000 n1p <- 50 zp <- c(rnorm(n1p, sd=5), rnorm(n-n1p, sd=1)) p <- 2*pnorm(-abs(zp)) # generate q zq <- c(rnorm(n1p, sd=4), rnorm(n-n1p, sd=1.2)) q <- 2*pnorm(-abs(zq)) df <- data.frame(p, q) stratified_qqplot(data_frame = df, prin_value_label = "p", cond_value_label = "q")