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

