GWASwithSLOPE.R
In geneSLOPE: Genome-Wide Association Study with SLOPE

## ---- results='hide', message=FALSE-------------------------------------------
library(geneSLOPE)
famFile <- system.file("extdata", "plinkPhenotypeExample.fam", package = "geneSLOPE")
mapFile <- system.file("extdata", "plinkMapExample.map", package = "geneSLOPE")
snpsFile <- system.file("extdata", "plinkDataExample.raw", package = "geneSLOPE")

## -----------------------------------------------------------------------------
phenotype <- read_phenotype(filename = famFile)

## ---- warning=FALSE-----------------------------------------------------------
screening.result <- screen_snps(snpsFile, mapFile, phenotype, pValMax = 0.05, 
                      chunkSize = 1e2, verbose=FALSE)

## -----------------------------------------------------------------------------
summary(screening.result)

## -----------------------------------------------------------------------------
clumping.result <- clump_snps(screening.result, rho = 0.3, verbose = FALSE)

## -----------------------------------------------------------------------------
summary(clumping.result)

## ---- warning=FALSE, fig.height=7, fig.width=7--------------------------------
plot(clumping.result)

## ---- warning=FALSE, fig.height=6, fig.width=6--------------------------------
plot(clumping.result, chromosomeNumber = 1)

## ---- eval=FALSE--------------------------------------------------------------
#  plot(clumping.result)
#  identify_clump(clumping.result)

## ---- warning=FALSE, fig.height=6, fig.width=6--------------------------------
plot(clumping.result, clumpNumber = 1)

## -----------------------------------------------------------------------------
slope.result <- select_snps(clumping.result, fdr=0.1)

## ---- warning = FALSE, fig.height=7, fig.width=7------------------------------
summary(slope.result)
plot(slope.result)

## ---- eval=FALSE--------------------------------------------------------------
#  plot(slope.result)
#  identify_clump(slope.result)

## ---- warning = FALSE, fig.height=7, fig.width=7------------------------------
plot(slope.result, clumpNumber = 1)

## -----------------------------------------------------------------------------
slope.result$selectedSnpsNumbers

## -----------------------------------------------------------------------------
slope.result$X_info[slope.result$selectedSnpsNumbers,]

## -----------------------------------------------------------------------------
summary(slope.result, clumpNumber = 1)