buildSpliceSites: Functions to query PALSdb

In splicegear: splicegear

Description

Functions to make a query on PALSdb, and build objects from the result of a query.

Usage

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)

Arguments

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.

Details

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).

Value

An object of class XML for queryPALSdb, an URL for getPALSdbURL or a list of objects of class SpliceSites.

Author(s)

[e-mail]

References

"Standardazed output for putative alternative splicing: application to the study of splice variants with microarrays", Gautier L. et al., 2003, manuscript in preparation.

See Also

queryPALSdb

Examples

library(XML)

filename <- system.file("extdata", "example.xml", package="splicegear")

xml <- xmlTreeParse(filename, asTree=TRUE)

spsites <- buildSpliceSites(xml)

splicegear documentation built on Oct. 31, 2019, 7:40 a.m.