bankSummary              package:GeneR              R Documentation

_C_o_m_p_u_t_e_s _i_n_f_o_r_m_a_t_i_o_n_s _o_n _a_l_l _a _b_a_n_k _f_i_l_e

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

     This functions computes informations (with function compoSeq,
     GCcontent, of seqSkew) on a complete bank file.

     It returns a data frame with one line by sequences in the bank
     file.

     Parameter "name" can be use to limit the exploration to only a few
     sequences.

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

     bankSummary(file, name = NULL, type = "F", fun = compoSeq, seqno = 0)

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

    file: Integer/scalar, File name of the bank (fasta file)

   seqno: Integer/scalar, Sequence number (buffer number)

    name: String/vector, Names of sequences in bank file, NULL: uses
          all sequences of the bank

    type: String/scalar, Bank format ("F" -> fasta. "E" -> embl, "G" ->
          GenBank)

     fun: Function, Function to be used (for example seqSkew

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

     a data frame with one line by sequence.

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

     Antoine Lucas

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

     'bankDensityProfile'

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

       for(i in 1:8)
       {
         s=randomSeq(n=100)
         placeString(s,seqno=0)
         writeFasta("toto_norm.fa",append=TRUE,name=i)
       }
       bankSummary(file="toto_norm.fa")
       bankSummary(file="toto_norm.fa",fun=seqSkew)

