## ----style, echo = FALSE, results = 'asis'------------------------------- knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")) ) options(width = 75) ## ---- message = FALSE---------------------------------------------------- library(SummarizedExperiment) ## ------------------------------------------------------------------------ library(airway) data(airway) airway ## ------------------------------------------------------------------------ set.seed(123) m <- matrix( rnorm(12), nrow = 4, ncol = 3, dimnames = list(letters[1:4], LETTERS[1:3]) ) m ## ------------------------------------------------------------------------ dim(m) dimnames(m) m[1:2, 2:1] m[1:2,] ## ------------------------------------------------------------------------ m[1,] m[,1] ## ------------------------------------------------------------------------ m[ 1, , drop = FALSE] ## ------------------------------------------------------------------------ m ## ------------------------------------------------------------------------ m + 1 ## ------------------------------------------------------------------------ abs(m + 1) ## ------------------------------------------------------------------------ colSums(m) rowMeans(m) ## ------------------------------------------------------------------------ colData(airway) ## ------------------------------------------------------------------------ airway$dex ## ------------------------------------------------------------------------ ridx <- rowMeans(m) > 0 m[ridx, , drop = FALSE] ## ------------------------------------------------------------------------ l <- list(a = 1:5, b = month.abb) ## ------------------------------------------------------------------------ names(l) length(l) l[c(2, 1)] l[2] # list of length 1, containing element 2 of original list l[[2]] # element 2 of original list ## ------------------------------------------------------------------------ lengths(l) ## ------------------------------------------------------------------------ r <- rowRanges(airway) ## ------------------------------------------------------------------------ genome(r) <- "GRCh37" seqinfo(r) ## ------------------------------------------------------------------------ rowRanges(airway) <- r ## ------------------------------------------------------------------------ seqinfo(airway) ## ---- message = FALSE---------------------------------------------------- library(dplyr) # %>% ## ------------------------------------------------------------------------ chr14 <- seqinfo(r) %>% as("GRanges") %>% subset(seqnames == "14") ## ------------------------------------------------------------------------ idx <- r %over% chr14 r[idx] ## ---- message = FALSE---------------------------------------------------- library(readr) library(tibble) ## ---- eval = FALSE------------------------------------------------------- ## pdata_file <- file.choos() # airway-sample-sheet.csv ## counts_file <- file.choose() # airway-read-counts.csv ## ---- echo = FALSE------------------------------------------------------- pdata_file <- system.file(package="BiocIntro", "extdata", "airway-sample-sheet.csv") counts_file <- system.file(package="BiocIntro", "extdata", "airway-read-counts.csv") ## ------------------------------------------------------------------------ pdata <- read_csv(pdata_file) counts <- read_csv(counts_file) ## ------------------------------------------------------------------------ pdata <- column_to_rownames(pdata, "Run") counts <- column_to_rownames(counts, "Run") se <- SummarizedExperiment(t(counts), colData = pdata) se ## ------------------------------------------------------------------------ sessionInfo()