getChroLocation {AnnBuilder} | R Documentation |
These functions are used by objects GP to extract chromosomal location and orientation data for genes using source files provided by Golden Path
getChroLocation(srcUrl, exten = gpLinkNGene(), sep = "\t", fromWeb = TRUE, raw = FALSE) getGPData(srcUrl, sep = "\t") gpLinkNGene(test = FALSE, fromWeb = TRUE) getCytoList(data) getCytoLoc(organism, srcUrl = paste(getSrcUrl("gp",organism), "/", "http://www.genome.ucsc.edu/goldenPath/mm4/database/" ))
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 |
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 |
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.
getChroLocation
returns a matrix with five or two columns.
getGPData
returns a matrix.
gpLinkNGene
returns a named vector.
Jianhua Zhang
## Not run: # 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") ## End(Not run)