| writeChrLength {AnnBuilder} | R Documentation |
These functions figure out the chromosome length and write the length and organism binary files to the data directory of the pacakge
writeChrLength(pkgName, pkgPath, chrLengths)
findChrLength(organism, srcUrl = getSrcUrl("GP", organism))
writeOrganism(pkgName, pkgPath, organism)
pkgName |
pkgName a character string for the name of a
data package or R library |
pkgPath |
pkgPath a character string for the path where
pkgname resides |
organism |
organism a character string for the name of the
organism of interests |
srcUrl |
srcUrl a character string for the url of the data
source used to create the binary file for chromosome length |
chrLengths |
chrLengths a named vector of integers with
the names being the chromosome numbers and the values of the vector
being the total lengths of chromosomes |
findChrLength extracts data from the source and figures
out the total length for each chromosome. The total length for a
chromosome is determined as the maximum chromosome location plus 1000.
writeChrLength writes the chromosome length data to the
data directory as a binary file.
writeOrganism writes the name of the organism to the
data directory as a binary file.
findChrLength returns a named vector of integers.
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide BioInformatics functionalities through R
Jianhua Zhang
if(interactive()){
path <- file.path(.path.package("AnnBuilder", "temp"))
dir.create(file.path(path, "test"))
dir.create(file.path(path, "test", "data"))
chrLength <- findChrLength("human")
writeChrLength("test", path, chrLength)
writeOrganism("test", path, "human")
list.files(file.path(path, "test", "data"))
unlink(file.path(path, "test"), TRUE)
}