## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], knitr = citation("knitr")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], awst = citation("awst")[1] ) ## ----"install", eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("awst") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----"citation"--------------------------------------------------------------- ## Citation info citation("awst") ## ----"start", message=FALSE, warning=FALSE------------------------------------ library(awst) library(airway) library(SummarizedExperiment) library(EDASeq) library(ggplot2) ## ----reading------------------------------------------------------------------ data(airway) airway ## ----filtering---------------------------------------------------------------- filter <- rowMeans(assay(airway)) >= 10 table(filter) se <- airway[filter,] ## ----raw_awst----------------------------------------------------------------- se <- awst(se) se plot(density(assay(se, "awst")[,1]), main = "Sample 1") ## ----genefilter--------------------------------------------------------------- filtered <- gene_filter(se) dim(filtered) ## ----pca---------------------------------------------------------------------- res_pca <- prcomp(t(assay(filtered, "awst"))) df <- as.data.frame(cbind(res_pca$x, colData(airway))) ggplot(df, aes(x = PC1, y = PC2, color = dex, shape = cell)) + geom_point() + theme_classic() ## ----full--------------------------------------------------------------------- assay(se, "fq") <- betweenLaneNormalization(assay(se), which="full") se <- awst(se, expr_values = "fq") res_pca <- prcomp(t(assay(se, "awst"))) df <- as.data.frame(cbind(res_pca$x, colData(airway))) ggplot(df, aes(x = PC1, y = PC2, color = dex, shape = cell)) + geom_point() + theme_classic() ## ----createVignette, eval=FALSE----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("awst_intro.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("awst_intro.Rmd", tangle = TRUE) ## ----reproduce1, echo=FALSE--------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE--------------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results="asis", echo=FALSE, warning=FALSE, message=FALSE----------------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))