Nothing
## ---- 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)
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