Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- eval = FALSE------------------------------------------------------------
# install.packages("devtools")
# devtools::install_github("fumi-github/omicwas")
## ---- eval = FALSE------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
# BiocManager::install("sva")
## ----setup--------------------------------------------------------------------
library(omicwas)
## -----------------------------------------------------------------------------
?ctassoc
## -----------------------------------------------------------------------------
data(GSE42861small)
X = GSE42861small$X
W = GSE42861small$W
Y = GSE42861small$Y
Y = Y[seq(1, 20), ] # for brevity
C = GSE42861small$C
## -----------------------------------------------------------------------------
?GSE42861small
## -----------------------------------------------------------------------------
result = ctassoc(X, W, Y, C = C,
test = "full")
result$coefficients
## -----------------------------------------------------------------------------
result = ctassoc(X, W, Y, C = C,
test = "nls.logit",
regularize = TRUE)
print(result$coefficients, n = 20)
## -----------------------------------------------------------------------------
data(GTExsmall)
X = GTExsmall$X
W = GTExsmall$W
Y = GTExsmall$Y + 1
Y = Y[seq(1, 20), ] # for brevity
C = GTExsmall$C
## -----------------------------------------------------------------------------
?GTExsmall
## -----------------------------------------------------------------------------
result = ctassoc(X, W, Y, C = C,
test = "full")
result$coefficients
## -----------------------------------------------------------------------------
result = ctassoc(X, W, Y, C = C,
test = "nls.log",
regularize = TRUE)
print(result$coefficients, n = 15)
## -----------------------------------------------------------------------------
?ctcisQTL
## -----------------------------------------------------------------------------
data(GSE79262small)
X = GSE79262small$X
Xpos = GSE79262small$Xpos
W = GSE79262small$W
Y = GSE79262small$Y
Ypos = GSE79262small$Ypos
C = GSE79262small$C
X = X[seq(1, 3001, 100), ] # for brevity
Xpos = Xpos[seq(1, 3001, 100)]
Y = Y[seq(1, 501, 100), ]
Ypos = Ypos[seq(1, 501, 100)]
## -----------------------------------------------------------------------------
?GSE79262small
## -----------------------------------------------------------------------------
ctcisQTL(X, Xpos, W, Y, Ypos, C = C)
## -----------------------------------------------------------------------------
head(
read.table(file.path(tempdir(), "ctcisQTL.out.txt"),
header = TRUE,
sep ="\t"))
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