Nothing
## ---- echo = FALSE, message = FALSE-------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(pander)
panderOptions('knitr.auto.asis', TRUE)
panderOptions('plain.ascii', TRUE)
## ---- eval=FALSE--------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE)) {
# install.packages("BiocManager")
# }
# BiocManager::install("BEclear")
## ---- eval=FALSE--------------------------------------------------------------
# if (!requireNamespace("devtools", quietly = TRUE)) {
# install.packages("devtools")
# }
# devtools::install_github("David-J-R/MoDentify")
## -----------------------------------------------------------------------------
library(BEclear)
## ----data---------------------------------------------------------------------
data("BEclearData")
## -----------------------------------------------------------------------------
knitr::kable(ex.data[1:10,1:5], caption = 'Some entries from the example data-set')
## -----------------------------------------------------------------------------
knitr::kable(ex.samples[1:10,], caption = 'Some entries from the example sample annotation')
## ----detection, cache=TRUE----------------------------------------------------
batchEffect <- calcBatchEffects(
data = ex.data, samples = ex.samples,
adjusted = TRUE, method = "fdr"
)
mdifs <- batchEffect$med
pvals <- batchEffect$pval
## ----summary, cache=TRUE------------------------------------------------------
summary <- calcSummary(medians = mdifs, pvalues = pvals)
knitr::kable(head(summary), caption = 'Summary over the batch affected gene-sample combination of the example data set')
## ----score, cache=TRUE--------------------------------------------------------
score <- calcScore(ex.data, ex.samples, summary, dir = getwd())
knitr::kable(score, caption = 'Batch scores of the example data-set')
## ----clearBE, cache=TRUE------------------------------------------------------
cleared.data <- clearBEgenes(ex.data, ex.samples, summary)
## ----imputation, cache=TRUE---------------------------------------------------
corrected.data <- imputeMissingData(cleared.data,
rowBlockSize = 60,
colBlockSize = 60, epochs = 50,
outputFormat = "", dir = getwd()
)
## ----replace, cache=TRUE------------------------------------------------------
corrected.data.valid<-replaceOutsideValues(corrected.data)
## ----correction, cache=TRUE---------------------------------------------------
result <- correctBatchEffect(data = ex.data, samples = ex.samples)
## -----------------------------------------------------------------------------
?BiocParallel::BiocParallelParam
## ----boxplot1, fig.wide = TRUE, fig.cap = "Distribution of the example beta values grouped by sample"----
makeBoxplot(ex.data, ex.samples, score,
bySamples = TRUE,
col = "standard", main = "Example data", xlab = "Batch",
ylab = "Beta value", scoreCol = TRUE)
## ----boxplot2, fig.wide = TRUE, fig.cap = "Distribution of the corrected beta values grouped by sample"----
makeBoxplot(corrected.data, ex.samples, score,
bySamples = TRUE,
col = "standard", main = "Corrected example data",
xlab = "Batch", ylab = "Beta value", scoreCol = FALSE)
## ----sessionInfo, echo=FALSE--------------------------------------------------
pander(sessionInfo(), compact=TRUE)
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