## ----dependencies, warning=FALSE, message=FALSE-------------------------- library(GenomicRanges) library(airway) ## ----biocLite, eval=FALSE------------------------------------------------ ## source("http://www.bioconductor.org/biocLite.R") ## biocLite(c("GenomicRanges", "airway")) ## ----airway-------------------------------------------------------------- library(airway) data(airway) airway ## ----colData------------------------------------------------------------- colData(airway) ## ----getColumn----------------------------------------------------------- airway$cell ## ----exptData------------------------------------------------------------ exptData(airway) ## ----names--------------------------------------------------------------- colnames(airway) head(rownames(airway)) ## ----assay--------------------------------------------------------------- airway assayNames(airway) assays(airway) head(assay(airway, "counts")) ## ----rowRanges----------------------------------------------------------- length(rowRanges(airway)) dim(airway) rowRanges(airway) ## ----numberOfExons------------------------------------------------------- length(rowRanges(airway)) sum(elementLengths(rowRanges(airway))) ## ----start--------------------------------------------------------------- start(rowRanges(airway)) start(airway) ## ----subsetByOverlaps---------------------------------------------------- gr <- GRanges(seqnames = "1", ranges = IRanges(start = 1, end = 10^7)) subsetByOverlaps(airway, gr) ## ----sessionInfo, echo=FALSE--------------------------------------------- sessionInfo()