Nothing
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
options(stringsAsFactors = FALSE)
## ---- eval = F, error = F, results='hide'--------------------------------
# install.packages(episcan)
## ---- echo = T, results='hide'-------------------------------------------
# load package
library(episcan)
## ---- echo = T, results='markup'-----------------------------------------
set.seed(321)
geno <- matrix(sample(0:2, size = 10000,
replace = TRUE, prob = c(0.5, 0.3, 0.2)), ncol = 100)
dimnames(geno) <- list(row = paste0("IND", 1:nrow(geno)),
col = paste0("rs", 1:ncol(geno)))
p <- c(rep(0, 60), rep(1, 40))
geno[1:5, 1:8]
## ---- echo = T, results='markup'-----------------------------------------
episcan(geno1 = geno,
pheno = p,
phetype = "case-control",
outfile = "episcan_1geno_cc",
suffix = ".txt",
zpthres = 0.9,
chunksize = 20,
scale = TRUE)
## ---- echo = T, results='markup'-----------------------------------------
result <- read.table("episcan_1geno_cc.txt",
header = TRUE,
stringsAsFactors = FALSE)
head(result)
## ---- echo = T, results='markup'-----------------------------------------
# simulate data
geno1 <- matrix(sample(0:2, size = 10000,
replace = TRUE, prob = c(0.5, 0.3, 0.2)), ncol = 100)
geno2 <- matrix(sample(0:2, size = 20000,
replace = TRUE, prob = c(0.4, 0.3, 0.3)), ncol = 200)
dimnames(geno1) <- list(row = paste0("IND", 1:nrow(geno1)),
col = paste0("rs", 1:ncol(geno1)))
dimnames(geno2) <- list(row = paste0("IND", 1:nrow(geno2)),
col = paste0("exm", 1:ncol(geno2)))
p <- rnorm(100)
# scan epistasis
episcan(geno1 = geno1,
geno2 = geno2,
pheno = p,
phetype = "quantitative",
outfile = "episcan_2geno_quant",
suffix = ".txt",
zpthres = 0.6,
chunksize = 50,
scale = TRUE)
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