## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------
BiocStyle::latex()


## ----preliminaries, echo=FALSE, message=FALSE----------------------------
library(GenomeInfoDb)


## ----genomeStyles1-------------------------------------------------------
seqmap <- genomeStyles()
head(seqmap,n=2)


## ----genomeStyles2-------------------------------------------------------
head(genomeStyles("Homo sapiens"),5)


## ----extractSeqlevels----------------------------------------------------
extractSeqlevels(species="Arabidopsis thaliana", style="NCBI")


## ----extractSeqlevelsgroup-----------------------------------------------
extractSeqlevelsByGroup(species="Arabidopsis thaliana", style="NCBI",
                         group="auto")


## ----seqlevelsStyle------------------------------------------------------
seqlevelsStyle(paste0("chr",c(1:30)))
seqlevelsStyle(c("2L","2R","X","Xhet"))


## ----keepChr-txdb--------------------------------------------------------
newchr <- paste0("chr",c(1:22,"X","Y","M","1_gl000192_random","4_ctg9_hap1"))
seqlevelsInGroup(newchr, group="sex")
seqlevelsInGroup(newchr, group="auto")
seqlevelsInGroup(newchr, group="linear")
seqlevelsInGroup(newchr, group="sex","Homo sapiens","UCSC")


## ----orderSeqlevels------------------------------------------------------
seqnames <- c("chr1","chr9", "chr2", "chr3", "chr10")
orderSeqlevels(seqnames)


## ----rankSeqlevels-------------------------------------------------------
seqnames <- c("chr1","chr9", "chr2", "chr3", "chr10")
rankSeqlevels(seqnames)


## ----find----------------------------------------------------------------
mapSeqlevels(c("chrII", "chrIII", "chrM"), "NCBI")