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# Chromosomes cytobands track from UCSC
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
# Example file : http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
track.bands.UCSC = function(
file,
name = "UCSC bands",
...
)
{
# Extraction
UCSC = utils::read.table(
file = file,
header = FALSE,
colClasses = c("character", "integer", "integer", "character", "character"),
col.names = c("chrom", "chromStart", "chromEnd", "name", "gieStain"),
sep = "\t",
quote = "",
comment.char = ""
)
# Rounding errors
UCSC[ UCSC$chromStart == 0 , "chromStart" ] = 1
# Chromosomes
chrom <- gsub(UCSC$chrom, pattern="^chr(.+)$", replacement="\\1")
# Track object
object <- track.bands(
# Columns
name = sprintf("%s%s", chrom, UCSC$name),
chrom = chrom,
start = as.integer(UCSC$chromStart),
end = as.integer(UCSC$chromEnd),
strand = factor(rep("+", nrow(UCSC)), levels=c("-","+")),
stain = UCSC$gieStain,
# Meta-data
.name = name,
...
)
return(object)
}
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