writeChrLength {AnnBuilder}R Documentation

Functions that creates binary files for chromosome length and organism

Description

These functions figure out the chromosome length and write the length and organism binary files to the data directory of the pacakge

Usage

writeChrLength(pkgName, pkgPath, chrLengths)
findChrLength(organism, srcUrl = getSrcUrl("GP", organism))
writeOrganism(pkgName, pkgPath, organism)

Arguments

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

Details

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.

Value

findChrLength returns a named vector of integers.

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide BioInformatics functionalities through R

Author(s)

Jianhua Zhang

References

See Also

ABPkgBuilder

Examples

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)
}

[Package AnnBuilder version 1.4.21 Index]