## ----dependencies, warning=FALSE, message=FALSE-------------------------- library(GenomeInfoDb) library(GenomicRanges) ## ----biocLite, eval=FALSE------------------------------------------------ ## source("http://www.bioconductor.org/biocLite.R") ## biocLite(c("GenomeInfoDb", "GenomicRanges")) ## ----seqlevelsForce------------------------------------------------------ gr <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(start = 1:2, end = 4:5)) seqlevels(gr, force=TRUE) <- "chr1" gr ## ----dropSeqlevels------------------------------------------------------- gr <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(start = 1:2, end = 4:5)) dropSeqlevels(gr, "chr1") keepSeqlevels(gr, "chr2") ## ----keepStandard-------------------------------------------------------- gr <- GRanges(seqnames = c("chr1", "chrU345"), ranges = IRanges(start = 1:2, end = 4:5)) keepStandardChromosomes(gr) ## ----GRanges------------------------------------------------------------- gr <- GRanges(seqnames = "chr1", ranges = IRanges(start = 1:2, width = 2)) ## ----seqStyle------------------------------------------------------------ newStyle <- mapSeqlevels(seqlevels(gr), "NCBI") gr <- renameSeqlevels(gr, newStyle) ## ----sessionInfo, echo=FALSE--------------------------------------------- sessionInfo()