| buildSpliceSites {splicegear} | R Documentation |
Functions to make a query on PALSdb, and build objects from the result of a query.
queryPALSdb(query, disp = c("data", "browser"),
field = c("keyword", "ug.id", "gb.id", "human.cytoband", "mouse.cytoband", "cluster_count"),
species = c("human", "mouse"),
e.value = "1e-1",
ident.threshold = c("90% 50b", "95% 50b", "90% 45b"))
getPALSdbURL(query, disp = c("data", "browser"),
field = c("keyword", "ug.id", "gb.id", "human.cytoband", "mouse.cytoband", "cluster_count"),
species = c("human", "mouse"),
e.value = "1e-1",
ident.threshold = c("90% 50b", "95% 50b", "90% 45b"))
buildSpliceSites(xml, verbose=TRUE)
query |
query string |
xml |
an object of class XML (as returned by
xmlTreeParse) |
disp |
(idem genbank and pubmed) |
field |
The field on which the query will be based |
species |
the specie to work with |
e.value |
E-value |
ident.threshold |
threshold for matching sequences |
verbose |
verbose output. |
queryPALSdb returns an an object of class XML when disp =
"data".
The function buildSpliceSites constructs SpliceSites
objects from the XML data. The variables in the slots
spsiteIpos.pData and spsiteIIpos.pData are at least
tissue (tissue information), histology and site
(site numbering).
An object of class XML for queryPALSdb, an URL for
getPALSdbURL or a list of objects of class SpliceSites.
laurent@cbs.dtu.dk
"Standardazed output for putative alternative splicing: application to the study of splice variants with microarrays", Gautier L. et al., 2003, manuscript in preparation.
library(XML)
filename <- system.file("data", "example.xml", package="splicegear")
xml <- xmlTreeParse(filename, asTree=TRUE)
spsites <- buildSpliceSites(xml)