rCGH (version 1.2.0)

hg19: Hg19 Chromosome Lengths and Centromere Locations

Description

A data set containing lengths and centromere locations for each of the 24 chromosomes, according to Hg19.

Usage

hg19

Value

Format

A data set with 24 rows and 5 columns:

• chrom: chromosome number.
• length: chromosome length.
• centromerStart: centromere start position.
• centromerEnd: centromere start position.
• cumlen: cumulative length (where the previous chromosome ends).

Source

These data derived from the Hg19 gap UCSC table, freely available at: UCSC Access date: 1-31-2014 Within the browser, select: group: All Tables database: hg19 table: gap

Examples

# For users convenience, we provide a prebuilt dataset
# containing the Hg19 chr lengths, and centromeres location.
hg19

# The same dataset can be obtained as follow:
## Not run: 
# library(BSgenome)
# library(rtracklayer)
# 
# getChrLength <- function(genome = "BSgenome.Hsapiens.UCSC.hg19"){
#     g <- getBSgenome(genome, masked=FALSE)
#     data.frame(chrom=1:24, length=seqlengths(g)[1:24])
# }
# .chrAsNum <- function(tbl){
#     tbl$chrom <- gsub("chr", "", tbl$chrom)
#     tbl$chrom[tbl$chrom=="X"] <- 23
#     tbl$chrom[tbl$chrom=="Y"] <- 24
#     tbl$chrom <- as.numeric(tbl$chrom)
#     tbl[order(tbl$chrom),]
# }
# getCentromeres <- function( genome="hg19" ){
#     mySession <- try(browserSession("UCSC"), silent=TRUE)
#     # In case of failure, try another mirror
#     if(inherits(mySession, "try-error"))
#         mySession <- browserSession("UCSC",
#                                     url="http://genome-euro.ucsc.edu/cgi-bin/")
#     genome(mySession) <- genome
#     obj <- ucscTableQuery(mySession, table="gap")
#     tbl <- getTable(obj)
#     tbl <- tbl[tbl$type=="centromere", c("chrom", "chromStart", "chromEnd")]
#     colnames(tbl)[2:3] <- c("centromerStart", "centromerEnd")
#     .chrAsNum(tbl)
# }
# makeHg19 <- function(){
#     tbl <- merge(getChrLength(), getCentromeres(), by="chrom")
#     cumlen <- c(0, cumsum(as.numeric(tbl$length))[-nrow(tbl)])
#     cbind.data.frame(tbl, cumlen=cumlen)    
# }
# hg19 <- makeHg19()
# hg19
# ## End(Not run)