getPathwayStatistics       package:sigPathway       R Documentation

_G_i_v_e _t_h_e _s_t_a_t_i_s_t_i_c_s _f_o_r _t_h_e _p_r_o_b_e _s_e_t_s _i_n _a _p_a_t_h_w_a_y

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

     Gives the statistics for the probe sets associated with a pathway.

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

     getPathwayStatistics(tab, phenotype, G, index, ngroups = 2,
                          statList = NULL, keepUnknownProbes = FALSE,
                          annotpkg = NULL)

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

     tab: a numeric matrix of expression values, with the rows and
          columns representing probe sets and sample arrays,
          respectively

phenotype: a numeric (or character if 'ngroups' >= 2) vector indicating
          the phenotype

       G: a list containing the source, title, and probe sets
          associated with each curated pathway

   index: an integer vector specifying the pathway(s) to summarize in
          'G'

 ngroups: an integer indicating the number of groups in the expression
          matrix

statList: a list containing results from 'calcTStatFast'

keepUnknownProbes: a boolean indicating whether to keep the names of
          probe sets not represented in tab in the summary data frame

annotpkg: a character vector specifying the name of the BioConductor
          annotation package to use to fetch accession numbers, Entrez
          Gene IDs, gene name, and gene symbols

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

     This function gives the mean, standard deviation, and test
     statistic for each probe in the pathway as indicated in
     'G[[index]]'.

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

     A list containing data frames (1 per pathway) with the probes'
     name, mean, standard deviation, the test statistic (e.g., t-test),
     and the corresponding unadjusted p-value.

     If 'ngroups' = 1, the Pearson correlation coefficient is also
     returned.

     If a valid 'annotpkg' is specified, the probes' accession numbers,
     Entrez Gene IDs, gene name, and gene symbols are also returned. 
     This option only works if the probes in the gene set list 'G' are
     manufacturer IDs corresponding to those used in making the
     BioConductor annotation package.

_N_o_t_e:

     See the help page of 'calculate.NTk' or 'calculate.NEk' for
     example code that uses 'getPathwayStatistics'

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

     Weil Lai

