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 using source files provided by Golden Path

Usage

getChroLocation(srcUrl, exten = gpLinkNGene(), sep = "\t", fromWeb =
TRUE, raw = FALSE)
getGPData(srcUrl, sep = "\t", ncol = 8, keep = c(3,7))
gpLinkNGene(test = FALSE, fromWeb = TRUE)
getCytoList(data)
getCytoLoc(organism, srcUrl = paste(getSrcUrl("gp",organism), "/",
          "http://www.genome.ucsc.edu/goldenPath/mm4/database/" ))

Arguments

srcUrl srcUrl a character string for the url where Golden Path 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 separator 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 location 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
organism organism a character string for the name of the organism of interest
data data a data matrix

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 five or two columns.
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")

[Package AnnBuilder version 1.4.21 Index]