buildSpliceSites         package:splicegear         R Documentation

_F_u_n_c_t_i_o_n_s _t_o _q_u_e_r_y _P_A_L_S_d_b

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

     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)

_A_r_g_u_m_e_n_t_s:

   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.

_D_e_t_a_i_l_s:

     '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).

_V_a_l_u_e:

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

_A_u_t_h_o_r(_s):

     laurent@cbs.dtu.dk

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

     'queryPALSdb'

_E_x_a_m_p_l_e_s:

     library(XML)

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

     xml <- xmlTreeParse(filename, asTree=TRUE)

     spsites <- buildSpliceSites(xml)

