Nothing
## ---- echo = FALSE, message = FALSE-------------------------------------------
knitr::opts_chunk$set(collapse = T, comment = "#>")
knitr::opts_chunk$set(fig.width=8, fig.height=5)
options(tibble.print_min = 4L, tibble.print_max = 4L)
#library(dplyr)
#library(ggplot2)
set.seed(1014)
## ---- eval=F------------------------------------------------------------------
# install.packages("devtools")
## ---- eval = F----------------------------------------------------------------
# library(devtools)
## ---- eval = F----------------------------------------------------------------
# install_github("camillemmoore/Power_Genetics", subdir="genpwr")
## -----------------------------------------------------------------------------
library(genpwr)
## -----------------------------------------------------------------------------
pw <- genpwr.calc(calc = "power", model = "logistic", ge.interaction = NULL,
N=400, Case.Rate=0.2, k=NULL,
MAF=seq(0.18, 0.25, 0.01), OR=c(3),Alpha=0.05,
True.Model=c("Dominant", "Recessive", "Additive"),
Test.Model=c("Dominant", "Recessive", "Additive", "2df"))
## -----------------------------------------------------------------------------
head(pw)
## -----------------------------------------------------------------------------
power.plot(pw)
## -----------------------------------------------------------------------------
pw <- genpwr.calc(calc = "power", model = "linear",
N=40, sd_y=4, k=NULL,
MAF=seq(0.18, 0.25, 0.01), ES=c(3),Alpha=0.05,
True.Model=c("Dominant", "Recessive", "Additive"),
Test.Model=c("Dominant", "Recessive", "Additive", "2df"))
## -----------------------------------------------------------------------------
ss <- genpwr.calc(calc = "ss", model = "logistic", ge.interaction = NULL,
OR=4, Case.Rate=0.4, k=NULL,
MAF=seq(0.3, 0.4, 0.02), Power=0.8, Alpha=0.05,
True.Model=c("Dominant", "Recessive", "Additive"),
Test.Model=c("Dominant", "Recessive", "Additive", "2df"))
## -----------------------------------------------------------------------------
ss.plot(ss)
## -----------------------------------------------------------------------------
or <- genpwr.calc(calc = "es", model = "logistic", ge.interaction = NULL,
N=1000, Case.Rate=0.4, k=NULL,
MAF=seq(0.30, 0.4, 0.02), Power=0.4, Alpha=0.05,
True.Model="All", Test.Model="All")
## -----------------------------------------------------------------------------
or.plot(or)
## -----------------------------------------------------------------------------
pec <- genpwr.calc(calc = "power", model = "logistic",
ge.interaction = "binary",
N=500, Case.Rate=0.3, MAF=seq(0.2,0.4,0.02), OR_G=3,
OR_E=3.5, OR_GE=4, P_e = 0.4,
Alpha=0.05, True.Model='All', Test.Model='All')
## -----------------------------------------------------------------------------
power.plot(pec)
## -----------------------------------------------------------------------------
pec <- genpwr.calc(calc = "power", model = "linear",
ge.interaction = "binary",
N=50, sd_y=3, MAF=seq(0.2,0.34,0.02), ES_G=3,
ES_E=1.5, ES_GE=2, P_e = 0.4,
Alpha=0.05, True.Model='All', Test.Model='All')
## -----------------------------------------------------------------------------
pec <- genpwr.calc(calc = "power", model = "logistic",
ge.interaction = "continuous",
N=500, Case.Rate=0.3, MAF=seq(0.25,0.31,0.02), OR_G=3,
OR_E=3.5, OR_GE=4, sd_e = 4,
Alpha=0.05, True.Model='All', Test.Model='All')
## -----------------------------------------------------------------------------
sse <- genpwr.calc(calc = "ss", model = "logistic", ge.interaction = "binary",
Power=0.5, Case.Rate=0.4, MAF=seq(0.3,0.4,0.05), OR_G=1.5,
OR_E=1.3, OR_GE=1.2, P_e = 0.4,
Alpha=0.05, True.Model="All", Test.Model="All")
## -----------------------------------------------------------------------------
ss.plot(sse)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.