posMaskedSeq              package:GeneR              R Documentation

_G_e_t _a_l_l _m_a_s_k_e_d _r_e_g_i_o_n_s

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

     This function return a matrix of masked postions from a fasta
     file. Masked regions are identified by lower case in fasta file.

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

     posMaskedSeq(file, name = NA, length = 10000)

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

    file: Fasta file path

    name: Name of sequence (if not: the first sequence from fasta file)

  length: Maximum number of regions to retrieve (default: 10000)

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

     a matrix of class intervals, of size nx2.

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

     Odile Rogier

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

     ## Make a dummy sequence
     s <- "ATGCtgTGTTagtacATTGGGTTTaAAA"
     placeString(s,upper=FALSE)
     writeFasta(file="toto.fa")
     posMaskedSeq("toto.fa")

