Nothing
## ----loadKnitr, echo=FALSE-----------------------------------------------
library("knitr")
# opts_chunk$set(eval=FALSE)
library(pander)
panderOptions("digits", 3)
set.seed(18090212)
library(shiftR)
## ----generateData--------------------------------------------------------
n = 1e6
sim = simulateBinary(n, corWithin = 0.99, corAcross = 0)
offsets = getOffsetsUniform(n = n, npermute = 10e3)
perm = shiftrPermBinary( sim$data1, sim$data2, offsets)
message("Fisher exact test p-value: ", perm$fisherTest$p.value)
message("Permutation p-value: ", perm$permPV)
## ----seed2, echo=FALSE---------------------------------------------------
set.seed(18090212)
## ----genPV---------------------------------------------------------------
n = 1e6
sim = simulatePValues(n, corWithin = 0.99, corAcross = 0)
## ----pvfish--------------------------------------------------------------
fisher.test(sim$data1 < 0.10, sim$data2 < 0.10)$p.value
## ----enr-----------------------------------------------------------------
enr = enrichmentAnalysis(
sim$data1,
sim$data2,
percentiles1 = c(0.01, 0.05, 0.10),
percentiles2 = c(0.01, 0.05, 0.10),
npermute = 10e3,
threads = 2)
message('Enrichment p-value is: ', enr$overallPV[2])
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