LL-class {AnnBuilder}R Documentation

Class "LL" a sub-class of pubRepo to handle data from LocusLink

Description

This class is a sub-class of pubRepo that is implemented specifically to parse data from LocusLink (ll_teml.gz)

Objects from the Class

Objects can be created by calls of the form new("LL", ...). A constructor (LL) is available and should be used to instatiate objects of LL

Slots

srcUrl:
Object of class "character", from class "pubRepo" a character string for the surce url where data will be downloaded/processed
parser:
Object of class "character", from class "pubRepo" a character string for the name of the file containing a segment of perl code with instructions on how the source data will be processed and output be generated
baseFile:
Object of class "character", from class "pubRepo" a character string for the name of the file that contains data that will be used as the base to process the source data. Data from the source that are related to elements in the base file will be extracted. baseFile is assumed to be a two folumn file with the first column being some type of arbitrary ids (e.g. Affymetrix probe ids) and the second cloumn being the corresponding ids of a given public repository (e.g. GenBank accession numbers or UniGene ids)

Extends

Class "pubRepo", directly.

Methods

No methods defined with class "LL" in the signature.

Note

This class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics funtionalities through R

Author(s)

Jianhua Zhang

References

www.ncbi.nlm.nih.gov/LocusLink

See Also

pubRepo-class

Examples

if(interactive()){
# Parse a truncated version of LL\_tmpl.gz from Bioconductor
path <- file.path(.path.package("AnnBuilder"), "scripts")
temp <- matrix(c("32469_f_at", "D90278", "32469_at", "L00693", "33825_at",
"X68733", "35730_at", "X03350", "38912_at", "D90042", "38936_at",
"M16652"), ncol = 2, byrow = TRUE)
write.table(temp, "tempfile", sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)  
ll <- LL(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz",
parser = file.path(path, "gbLLParser"), baseFile = "tempfile")
data <- parseData(ll)
unlink("tempfile")
}

[Package AnnBuilder version 1.4.21 Index]