gseaAnalysis            package:RNAither            R Documentation

_P_e_r_f_o_r_m _a _G_S_E_A _a_n_a_l_y_s_i_s _o_f _a _l_i_s_t _o_f _g_e_n_e_s

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

     Performs a GSEA analysis of a list of genes using the package '
     topGO' (see References).

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

     gseaAnalysis(hitVector, whichOnto)

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

hitVector: a named hit vector as generated by 'hitselectionZscore' or
          'hitselectionPval' 

whichOnto: One of the three GO ontologies: ' "biological_process"', '
          "molecular_function"' or ' "cellular_component"' 

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

     A table containing the enriched GO terms and their significance.

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

     A. Alexa, J. Rahnenfuhrer and T. Lengauer. Improved scoring of
     functional groups from gene expression data by decorrelating GO
     graph structure. Bioinformatics, 22(13):1600-1607, 2006

     Adrian Alexa and Jorg Rahnenfuhrer (2006). topGO: Enrichment
     analysis for Gene Ontology. R package version 1.4.0.

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

     'Ttest'

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

     data(scoredDataset1, package="RNAither")
     data(pValVec1, package="RNAither")

     ##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

     scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "Hits1", 0.1, 
     "GeneName", "pvalue_testfile1.txt")
     hitVector1 <- scoredHits1[[2]]
     gseaTable <- gseaAnalysis(hitVector1, "biological_process")

