GOstats-package           package:GOstats           R Documentation

_T_o_o_l_s _f_o_r _m_a_n_i_p_u_l_a_t_i_n_g _G_O _a_n_d _m_i_c_r_o_a_r_r_a_y_s.

_D_e_s_c_r_i_p_t_i_o_n:

     A set of tools for interacting with GO and microarray data. A
     variety of basic manipulation tools for graphs, hypothesis testing
     and other simple calculations.

_D_e_t_a_i_l_s:


       Package:    GOstats
       Version:    1.7.4
       Date:       23-08-2006
       biocViews:  Statistics, Annotation, GO, MultipleComparisons
       Depends:    graph (>= 1.9.25), GO, annotate, RBGL, xtable, Biobase, genefilter, multtest, Category (>= 1.3.7), methods
       Imports:    methods, Category
       Suggests:   hgu95av2 (>= 1.6.0)
       License:    Artistic

     Index:


     ALL                     Acute Lymphoblastic Leukemia Data from the
     Ritz
                             Laboratory
     GOLeaves                Identify the leaves in a GO Graph
     GOstats-defunct         Defunct Functions in GOstats Package
     Ndists                  Distance matrices for the BCR/ABL and NEG
                             subgroups.
     compCorrGraph           A function to compute a correlation based
     graph
                             from Gene Expression Data
     compGdist               A function to compute the distance between
                             pairs of nodes in a graph.
     dropECode               Drop GO labels for specified Evidence
     Codes
     getEvidence             Get the Evidence codes for a set of GO
     terms.
     getGOTerm               Functions to Access GO data.
     getOntology             Get GO terms for a specified ontology
     hasGOannote             Check for GO annotation
     hyperG2Affy             A List of Affymetrix IDs from GOIDs
     hyperGtable             Table from GOHyperG
     idx2dimnames            Index to Dimnames
     makeGOGraph             Construct a GO Graph
     notConn                 Find genes that are not connected to the
                             others.
     oneGOGraph              Construct the GO graph given a set of
     leaves.
     shortestPath            Shortest Path Analysis
     simLL                   Functions to compute similarities between
     GO
                             graphs and also between Entrez Gene IDs
     based on
                             their induced GO graphs.
     triadCensus             Triad Functions

     Further information is available in the following vignettes:

       'GOstats'  Using GOstats (source, pdf)
       'GOusage'  Basic GO Usage (source, pdf)
       'GOvis'    Visualizing Data Using GOstats (source, pdf)

_A_u_t_h_o_r(_s):

     R. Gentleman with contributions from S. Falcon

     Maintainer: R. Gentleman <rgentlem@fhcrc.org>

