plot.glide: A function used to draw the q-q plot

In GLIDE: Global and Individual Tests for Direct Effects

A function used to draw the q-q plot

Description

It is used to draw the q-q plot

Usage

## S3 method for class 'glide'
plot(x,qcutoff=0.2,xlab="Expected null p-values (log base 10)",
                       ylab="Observed p-values (log base 10)",...)

Arguments

x	x is a dataframe, it is the outcome of the glide function.
qcutoff	qcutoff is the q-value cutoff.
xlab	xlab is the default x label.
ylab	ylab is the default y label.
...	the rest plot arguments.

Value

No return value, q-q plot will be generated.

Author(s)

James Y. Dai and X. Wang

Examples

##first generate output using the glide function
#load an example data
data(simdata)
simdat=simdata$simdat
coeff=simdata$coeff

formula=as.formula("outcome~age+sex+pc1+pc2+pc3")
genotype_columns=which(grepl("^SNP",colnames(simdat)))

#run glide
out=glide(formula=formula,exposure_coeff=coeff,genotype_columns,data=simdat,np=100000,
qcutoff=0.2,parallel=TRUE,corenumber=1,verbose=TRUE)

##draw the plot
plot.glide(out)

GLIDE documentation built on May 28, 2022, 1:08 a.m.