Nothing
## ----reqs, echo=FALSE, message=FALSE------------------------------------------
suppressMessages(library(tmle))
suppressMessages(library(minfi))
suppressMessages(library(SummarizedExperiment))
## ----prelims------------------------------------------------------------------
library(methyvim)
library(methyvimData)
## ----get-data-----------------------------------------------------------------
set.seed(479253)
data(grsExample)
grsExample
var_int <- as.numeric(colData(grsExample)[, 1])
table(var_int)
## ----make-methytmle-----------------------------------------------------------
mtmle <- .methytmle(grsExample)
## ----methyvim-ate-sl----------------------------------------------------------
suppressMessages(
methyvim_ate_sl <- methyvim(data_grs = grsExample, sites_comp = 25,
var_int = var_int, vim = "ate", type = "Mval",
filter = "limma", filter_cutoff = 0.10,
parallel = FALSE, tmle_type = "sl"
)
)
## ----methyvim-ate-sl-print----------------------------------------------------
vim(methyvim_ate_sl)
## ----methyvim-ate-glm---------------------------------------------------------
suppressMessages(
methyvim_ate_glm <- methyvim(data_grs = grsExample, sites_comp = 25,
var_int = var_int, vim = "ate", type = "Mval",
filter = "limma", filter_cutoff = 0.10,
parallel = FALSE, tmle_type = "glm"
)
)
## ----methyvim-ate-glm-print---------------------------------------------------
vim(methyvim_ate_glm)
## ----methyvim-rr-sl-----------------------------------------------------------
methyvim_rr_sl <- methyvim(data_grs = grsExample, sites_comp = 25,
var_int = var_int, vim = "rr", type = "Mval",
filter = "limma", filter_cutoff = 0.10,
parallel = FALSE, tmle_type = "sl"
)
## ----methyvim-rr-sl-print-----------------------------------------------------
vim(methyvim_rr_sl)
## ----methyvim-rr-glm----------------------------------------------------------
methyvim_rr_glm <- methyvim(data_grs = grsExample, sites_comp = 25,
var_int = var_int, vim = "rr", type = "Mval",
filter = "limma", filter_cutoff = 0.10,
parallel = FALSE, tmle_type = "glm"
)
## ----methyvim-rr-glm-print----------------------------------------------------
vim(methyvim_rr_glm)
## ----setup-minfidata----------------------------------------------------------
suppressMessages(library(minfiData))
data(MsetEx)
mset <- mapToGenome(MsetEx)
grs <- ratioConvert(mset)
grs
## ---- minfidata-maketx--------------------------------------------------------
var_int <- (as.numeric(as.factor(colData(grs)$status)) - 1)
table(var_int)
## ---- minfidata-methyvim, eval=FALSE------------------------------------------
# suppressMessages(
# methyvim_cancer_ate <- methyvim(data_grs = grs, var_int = var_int,
# vim = "ate", type = "Beta", filter = "limma",
# filter_cutoff = 0.30, obs_per_covar = 2,
# parallel = FALSE, sites_comp = 50,
# tmle_args = list(cv_folds = 2),
# tmle_type = "sl"
# )
# )
## ----vim-cancer-ate, eval=FALSE-----------------------------------------------
# methyvim_cancer_ate
## ----fdr-msa, eval=FALSE------------------------------------------------------
# fdr_p <- fdr_msa(pvals = vim(methyvim_cancer_ate)$pval,
# total_obs = nrow(methyvim_cancer_ate))
## ----methyvim-pvals-both, eval=FALSE------------------------------------------
# plot(methyvim_cancer_ate)
## ----methyvim-volcano, eval=FALSE---------------------------------------------
# methyvolc(methyvim_cancer_ate)
## ----methyvim-heatmap, eval=FALSE---------------------------------------------
# methyheat(methyvim_cancer_ate)
## ----session-info, echo=FALSE-------------------------------------------------
sessionInfo()
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