LL-class {AnnBuilder} | R Documentation |
This class is a sub-class of pubRepo that is implemented specifically to parse data from LocusLink (ll_teml.gz)
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
srcUrl
:"character", from class
"pubRepo"
a character string for the surce url where data
will be downloaded/processedparser
:"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 generatedbaseFile
:"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)
Class "pubRepo"
, directly.
No methods defined with class "LL" in the signature.
Jianhua Zhang
www.ncbi.nlm.nih.gov/LocusLink
## Not run: # 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") ## End(Not run)