getImat                package:pcot2                R Documentation

_G_e_n_e_r_a_t_e _a_n _i_n_d_i_c_a_t_o_r _m_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

     This function is used to generate an indicator matrix as an input
     to the pcot2 function. The gene category indicator matrix
     indicates presence or absence of genes in pre-defined gene sets
     (e.g., gene pathways). The indicator matrix contains rows
     representing gene identifiers of genes present in the expression
     data and columns representing pre-defined group names. A value of
     1 indicates the presence of a gene and 0 indicates the absence for
     the gene in a particular group.

_U_s_a_g_e:

     getImat(x, pathlist, ms = 10)

_A_r_g_u_m_e_n_t_s:

       x: A matrix with no missing values; Each row represents a gene
          and each column represents a sample.

pathlist: A list of gene sets. 

      ms: The minimum gene set size. Gene sets containing less than
          this number of genes will be excluded from the analysis.

_V_a_l_u_e:

     An indicator matrix is returned. The matrix value is 1 (gene in)
     or 0 (gene out)

_A_u_t_h_o_r(_s):

     Sarah Song and Mik Black

_R_e_f_e_r_e_n_c_e_s:

     S.Song and M.Black (2006) PCOT2: an R package for assessing
     expression changes in groups of related genes. Submitted to
     Bioinformatics.

_S_e_e _A_l_s_o:

     'pcot2','corplot','corplot2','aveProbe'

_E_x_a_m_p_l_e_s:

     library(multtest)
     library(hu6800)  
     data(golub)
     rownames(golub) <- golub.gnames[,3]
     colnames(golub) <- golub.cl
     KEGG.list <- as.list(hu6800PATH)
     imat <- getImat(golub, KEGG.list, ms=10) 

