posMaskedSeq              package:GeneR              R Documentation

_P_o_s_i_t_i_o_n _o_f _m_a_s_k_e_d _f_r_a_g_m_e_n_t_s

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

     These functions return the position of masked fragments within a
     sequence. Masked fragments are identified by lower case letters or
     by specific characters (for example: 'N').

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

     posMaskedSeq(seqno=0,from = 1, to = 0, max = 10000,type= "lower")
     posMaskedSeqFile(file, name = NA, from = 1, to = 0, max = 10000)

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

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

 from,to: Integer/vector, Absolute addresses of the begin and the end
          of the fragments, (1 means the first nucleotide and 0
          conventionally the last one; from must not be larger than to)

    file: String/scalar, Path and file name of the Fasta sequence bank

    name: Name of the sequence (if NA: the first sequence of the bank)

    type: type of masked nucleotide i.e. "lower" or any character like
          "N"  (if lower, posMaskedSeq looks for lower case letters; if
          a character, posMaskedSeq looks for this character

     max: Maximum number of fragments to retrieve (default: 10000)

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

     a matrix of size n,2.

     gives a warning if there is more than max regions.

     return numeric(0) when no regions found.

_N_o_t_e:

     This function returns by default only 10000 first regions (default
     parameter max).

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

     Odile Rogier and Antoine Lucas

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

     See also 'mask',  'upperSeq',  'lowerSeq'

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

     ## Make a dummy sequence
     s <- "ATGCtgTGTTagtacATNNNNNNNNNNNNNNNTGGGTTTaAAAattt"
     placeString(s,upper=FALSE,seqno=0)
     posMaskedSeq(seqno=0,type="upper")
     posMaskedSeq(seqno=0,type="lower")

     ## Not run: 
     posMaskedSeq(seqno=0,type="lower",max=2)
     ## End(Not run)
     posMaskedSeq(seqno=0,type="N")

     writeFasta(file="toto.fa")
     posMaskedSeqFile("toto.fa")

