## ---- echo = FALSE, message = FALSE------------------------------------------- knitr::opts_chunk$set(collapse = TRUE, comment = "#>") library(pander) panderOptions('knitr.auto.asis', TRUE) panderOptions('plain.ascii', TRUE) ## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # BiocManager::install("BEclear") ## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("devtools", quietly = TRUE)) { # install.packages("devtools") # } # devtools::install_github("uds-helms/BEclear") ## ----------------------------------------------------------------------------- library(BEclear) ## ----data--------------------------------------------------------------------- data("BEclearData") ## ----------------------------------------------------------------------------- knitr::kable(ex.data[1:10,1:5], caption = 'Some entries from the example data-set') ## ----------------------------------------------------------------------------- knitr::kable(ex.samples[1:10,], caption = 'Some entries from the example sample annotation') ## ----detection, cache=TRUE---------------------------------------------------- batchEffect <- calcBatchEffects( data = ex.data, samples = ex.samples, adjusted = TRUE, method = "fdr" ) mdifs <- batchEffect$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--------------------------------------------------- library(ids) 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)