## ----style, echo = FALSE, results = 'asis'--------------------------------- knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))) ## -------------------------------------------------------------------------- x <- rnorm(50) y <- x + rnorm(50) df <- data.frame(Indep = x, Dep = y) fit <- lm(Dep ~ Indep, df) summary(fit) ## ---- warning=FALSE-------------------------------------------------------- library(ggplot2) ggplot(df, aes(x = Dep, y = Indep)) + geom_point() + geom_smooth(method="lm") ## -------------------------------------------------------------------------- suppressPackageStartupMessages({ library(Biostrings) }) dna <- DNAStringSet( c("AAACTG", "CCCAACCA") ) dna reverseComplement(dna) ## -------------------------------------------------------------------------- suppressPackageStartupMessages({ library(GenomicRanges) }) gr <- GRanges( c("chr1:10-19", "chr1:15-24", "chr1:30-39") ) gr ## -------------------------------------------------------------------------- width(gr) ## -------------------------------------------------------------------------- shift(gr, 1) shift(gr, c(1, 2, 3)) ## -------------------------------------------------------------------------- gaps(gr) reduce(gr) disjoin(gr) as(coverage(gr), "GRanges") ## -------------------------------------------------------------------------- snps <- GRanges("chr1", IRanges(c(7, 12, 17, 22), width = 1)) snps countOverlaps(gr, snps) subsetByOverlaps(snps, gr) ## -------------------------------------------------------------------------- gr$p.value <- runif(3) gr ## -------------------------------------------------------------------------- gene <- c("A", "A", "B") grl <- splitAsList(gr, gene) grl ## -------------------------------------------------------------------------- gr1 <- unlist(grl, use.names=FALSE) gr1$neg.log10.pvalue <- -log10(gr1$p.value) relist(gr1, grl) ## -------------------------------------------------------------------------- suppressPackageStartupMessages({ library(airway) }) data(airway) airway ## -------------------------------------------------------------------------- colData(airway) airway[, airway$dex == "trt"] ## -------------------------------------------------------------------------- rowRanges(airway) rowData(airway)$p.value <- runif(nrow(airway)) ## -------------------------------------------------------------------------- libSize <- colSums(assay(airway)) libSize airway$libSize <- libSize table(rowSums(assay(airway)) != 0) ## -------------------------------------------------------------------------- suppressPackageStartupMessages({ library(org.Hs.eg.db) }) rowData(airway)$Symbol <- mapIds( org.Hs.eg.db, rownames(airway), "SYMBOL", "ENSEMBL" ) ## ---- warning=FALSE, message=FALSE----------------------------------------- suppressPackageStartupMessages({ library(AnnotationHub) library(ExperimentHub) }) query(AnnotationHub(), c("Homo sapiens", "gtf", "release-90")) query(AnnotationHub(), "EnsDb") query(ExperimentHub(), "curatedMetagenomic")