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 list, vector or file 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(keyword.list, present.genes=, GO.ont=)
       getCmatrix(gene.list, present.genes=, min.size=, max.size=)
       getCmatrix(vector=, delimiter=, as.matrix=)
       getCmatrix(file=, delimiter=, ...)

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

keyword.list: A list containing character vectors for each keyword that
          specify the gene members. 

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

  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.  

  GO.ont: "CC","BP",or "MF" specify the ontology to limit categories
          to. 

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

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

as.matrix: Optional argument to specify a matrix is returned rather
          than a matrix.csr.

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

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

C.mat.csr: If 'as.matrix=F' a sparse matrix is returned with the rows
          corresponding  to the genes and columns are categories

row.names: Character vector of gene names

col.names: Character vector of category names

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

     William T. Barry: bill.barry@duke.edu

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

     W. T. Barry, A. B. Nobel and F.A. Wright, 2005, _Significance
     Analysis of functional categories in gene expression studies: a
     structured permutation approach_, _Bioinformatics_ {\bf 21}(9)
     1943-9. 

     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 = ";",
                as.matrix=TRUE)

