getChroLocation {AnnBuilder}R Documentation

Functions to extract data from golden path

Description

These functions are used by objects GP to extract chromosomal location and orientation data for genes.

Usage

getChroLocation(srcUrl, exten = gpLinkNGene(), sep = "\t", fromWeb =
TRUE, raw = FALSE)
getGPData(srcUrl, sep = "\t", ncol = 8, keep = c(3,7))
gpLinkNGene(test = FALSE)

Arguments

srcUrl srcUrl a character string for the url where source data are available
exten exten a character string for the name of the file to be used for the extraction
sep sep a character string for the separater used by the source file
ncol ncol an integer for the total number of columns a source data set has
keep keep a numeric vector for the columns (defined by column number) to be kept
test test a boolean to indicate whether the process is in a testing mode
fromWeb fromWeb a boolean to indicate whether the source data should be downloaded from the web or is a local file
raw raw a boolean indicating whether chromosomal loation data will be returned as a five column data frame with ID, Chromosome, strand, start, and end or a two column data with ID and processed chromosome location data

Details

getChroLocation extracts chromosomal location data from a data file named refGene.

getGPData Reads data from a source data file defined by srcUrl and returns them as a matrix.

gpLinkNGene returns a correct link and gene data file names that will be used to get chromosomal location data.

Value

getChroLocation returns a matrix with the first column being LocusLink ids, the second being the chromosomal location, and third being the orientation for that locus.
getGPData returns a matrix.
gpLinkNGene returns a named vector.

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

http://www.genome.ucsc.edu

See Also

GP

Examples

# Truncated versions of files stored in Bioconductor site are used
gpLinkNGene(test = FALSE)
temp <- getGPData(
"http://www.bioconductor.org/datafiles/wwwsources/Tlink.txt",
sep = "\t", ncol = 8, keep = c(3,7))
temp <- getChroLocation(
"http://www.bioconductor.org/datafiles/wwwsources/",
exten = gpLinkNGene(TRUE), sep = "\t")

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