getCmatrix               package:safe               R Documentation

_G_e_n_e_r_a_t_i_o_n _o_f _a _C _m_a_t_r_i_x

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

     This function will convert a text file, vector or list of gene
     annotation into a C matrix. Size constraints, and present/absent
     calls can be set to filter  categories and genes accordingly.

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

       getCmatrix(list, present.genes=, min.size=, max.size=)
       getCmatrix(vector=, delimiter=)
       getCmatrix(file=, delimiter=, ...)

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

    list: A list containing character vectors for each gene that
          specify the functional categories it belongs to by keywords. 

  vector: A character vector of gene annotation with a specified
          delimiter between category keywords. 

    file: A file containing the character vector of gene annotation. 

delimiter: Delimiter used between category keywords when provided as a
          vector or file. 

present.genes: An optional vector used to filter genes in the C matrix.
          Can be  provided as an unordered character vector of gene
          names that match 'names(list)', or as an ordered vector of
          presence ('1') and absence ('0') calls.  

min.size: Optional minimum category size to be considered. 

max.size: Optional maximum category size to be considered. 

     ...: Any extra arguments will be forwarded to the read.table
          function when category assigments are given as a file.

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

     A matrix is returned with the rows corresponding to the genes as
     labeled by 'names(list)' and each column corresponding to a
     category.

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

     William T. Barry: wbarry@bios.unc.edu

_R_e_f_e_r_e_n_c_e_s:

     W. T. Barry, A. B. Nobel and F.A. Wright, 2004, _Significance
     Analysis of functional categories in gene expression studies: a
     structured permutation approach_, _Bioinformatics_ In press. 

     See also the vignette included with this package.

_S_e_e _A_l_s_o:

     {'safe', 'safeplot',  'getPImatrix',.}

_E_x_a_m_p_l_e_s:

     ## A simple illustration
     anno <- c("Keyword1","Keyword2;Keyword3","",
               "Keyword3;Keyword1","Keyword3")
     names(anno) <- paste("Gene",1:5)

     getCmatrix(vector = anno, delimiter = ";")

