Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## -----------------------------------------------------------------------------
library(onlineFDR)
sample.df <- data.frame(
id = c('A15432', 'B90969', 'C18705', 'B49731', 'E99902',
'C38292', 'A30619', 'D46627', 'E29198', 'A41418',
'D51456', 'C88669', 'E03673', 'A63155', 'B66033'),
date = as.Date(c(rep("2014-12-01",3),
rep("2015-09-21",5),
rep("2016-05-19",2),
"2016-11-12",
rep("2017-03-27",4))),
pval = c(2.90e-14, 0.06743, 0.01514, 0.08174, 0.00171,
3.61e-05, 0.79149, 0.27201, 0.28295, 7.59e-08,
0.69274, 0.30443, 0.000487, 0.72342, 0.54757))
set.seed(1)
results <- LORD(sample.df)
results
## -----------------------------------------------------------------------------
set.seed(1); results.indep <- LOND(sample.df) # for independent p-values
set.seed(1); results.dep <- LOND(sample.df, dep=TRUE) # for dependent p-values
# compare adjusted significance thresholds
cbind(independent = results.indep$alphai, dependent = results.dep$alphai)
## -----------------------------------------------------------------------------
set.seed(1); results.LORD.plus <- LORD(sample.df)
set.seed(1); results.LORD3 <- LORD(sample.df, version=3)
set.seed(1); results.LORD.discard <- LORD(sample.df, version='discard')
set.seed(1); results.LORD.dep <- LORD(sample.df, version='dep')
# compare adjusted significance thresholds
cbind(LORD.plus = results.LORD.plus$alphai,
LORD3 = results.LORD3$alphai,
LORD.discard = results.LORD.discard$alphai,
LORD.dep = results.LORD.dep$alphai)
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