getPathwayStatistics.NGSk     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.NGSk(statV, probeID, G, index,
                               keepUnknownProbes = FALSE, annotpkg = NULL)

_A_r_g_u_m_e_n_t_s:

   statV: a numeric vector of test statistic (not p-values) for each
          individual probe/gene

 probeID: a character vector containing the names of probe sets
          associated with a matrix of expression values

       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'

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 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 and the corresponding test statistic.

     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 for 'calculate.NGSk' for example code that uses
     'getPathwayStatistics.NGSk'

_A_u_t_h_o_r(_s):

     Weil Lai

