yeastPkgBuilder {AnnBuilder} | R Documentation |
These functions builds a data package for yeast genome using data from Yeast Genome web site of Stanford University, KEGG, and Gene Ontology.
yeastPkgBuilder(pkgName, pkgPath, base="", version, author, fromWeb=TRUE, lazyLoad=TRUE)
pkgName |
pkgName a character string for the name of the
data package to be built |
base |
base a matrix with two columns with the first one
being probe ids and the second one being their mappings to ORF (Open
Reading Frame) ids. Columns have the name "probe" and "orf" |
pkgPath |
pkgPath a character string for the directory
where the data package to be built will be stored |
version |
version a character string for the version
number of the data package to be built |
author |
author a named vector of two character strings
with a name element for the name and an address element of email
address of the maintainer of the data package |
fromWeb |
fromWeb a boolean to indicate whether the data
from GO should be downloaded from the web or read locally. The url
for GO should be the file name of a local file if fromWeb is
FALSE. For windows users, the data file from GO should be
downloaded/unzipped manually and set the url for GO to be the name
of the local file |
lazyLoad |
lazyLoad a boolean indicating whether a lazy
load database will be created |
Annotation elements are limited to those provided by Yeast Genome (gene name, chromosome number, chromosomal location, GO id, and evidence code), KEGG (path and enzyme data) and GO (GO mappings)
findYGChrLength
returns a named vector of integers with
chromosome numbers names and length of chromosomes as values.
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang
# Not provided.