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.

_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

