plot.sffdr: Plotting function for sffdr object

In sffdr: Surrogate Functional False Discovery Rates for Genome-Wide Association Studies

Plotting function for sffdr object

Description

Graphical display of the sffdr object

Usage

## S3 method for class 'sffdr'
plot(x, rng = c(0, 5e-08), ...)

Arguments

x	A sffdr object.
rng	Significance region to show. Optional.
...	Additional arguments. Currently unused.

Value

Plotting function to summarize significance results from sffdr.

Author(s)

Andrew J. Bass

See Also

sffdr

Examples

# import data
data(bmi)

# separate main p-values and conditioning p-values
p <- sumstats$bmi
z <- as.matrix(sumstats[, -1])

# apply pi0_model to create model
knots <- c(0.005, 0.01, 0.025, 0.05, 0.1)
fmod <- pi0_model(z, knots = knots)

# estimate functional pi0
fpi0_out <- fpi0est(p, z = fmod$zt, pi0_model = fmod$fmod)
fpi0 <- fpi0_out$fpi0

# apply sffdr
# Note all tests are independent see 'indep_snps' argument
# The very small p-values, set epsilon to min of p
sffdr_out <- sffdr(p, fpi0, epsilon = min(p))

# Plot significance results
plot(sffdr_out, rng = c(0, 5e-4))

sffdr documentation built on April 4, 2025, 1:41 a.m.