########################################################################################################################
## createAnnotationPackage.rn5.R
## created: 2014-02-13
## creator: Yassen Assenov
## ---------------------------------------------------------------------------------------------------------------------
## Annotation package creation for Rn5.
########################################################################################################################
## F U N C T I O N S ###################################################################################################
#' createAnnotationPackage.rn5
#'
#' Helper function to create RnBeads annotation package for genome assembly rn5.
#'
#' @return None (invisible \code{NULL}).
#' @author Yassen Assenov
#' @noRd
createAnnotationPackage.rn5 <- function() {
suppressPackageStartupMessages(require(BSgenome.Rnorvegicus.UCSC.rn5))
## Genomic sequence and supported chromosomes
GENOME <- "BSgenome.Rnorvegicus.UCSC.rn5"
assign('GENOME', GENOME, .globals)
CHROMOSOMES <- c(1:20, "X")
names(CHROMOSOMES) <- paste0("chr", CHROMOSOMES)
assign('CHROMOSOMES', CHROMOSOMES, .globals)
rm(GENOME)
## Download SNP annotation
logger.start("SNP Annotation")
vcf.files <- gsub("^chr(.+)$", "vcf_chr_\\1.vcf.gz", names(CHROMOSOMES))
vcf.files <- paste0(DBSNP.FTP.BASE, "rat_10116/VCF/", vcf.files)
update.annot("snps", "polymorphism information", rnb.update.dbsnp, ftp.files = vcf.files)
logger.info(paste("Using:", attr(.globals[['snps']], "version")))
rm(vcf.files)
logger.completed()
## Define genomic regions
biomart.parameters <- list(
database.name = "ENSEMBL_MART_ENSEMBL",
dataset.name = "rnorvegicus_gene_ensembl",
required.columns = c(
"id" = "ensembl_gene_id",
"chromosome" = "chromosome_name",
"start" = "start_position",
"end" = "end_position",
"strand" = "strand",
"symbol" = "rgd_symbol",
"entrezID" = "entrezgene"),
host = "mar2015.archive.ensembl.org")
logger.start("Region Annotation")
update.annot("regions", "region annotation", rnb.update.region.annotation,
biomart.parameters = biomart.parameters)
rm(biomart.parameters)
logger.completed()
## Define genomic sites
logger.start("Genomic Sites")
update.annot("sites", "CpG annotation", rnb.update.sites)
logger.completed()
## Create all possible mappings from regions to sites
logger.start("Mappings")
update.annot("mappings", "mappings", rnb.create.mappings)
logger.completed()
## Export the annotation tables
rnb.export.annotations.to.data.files()
}
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