Concat                 package:GeneR                 R Documentation

_C_o_n_c_a_t_e_n_a_t_i_o_n _o_f _t_w_o _s_e_q_u_e_n_c_e_s

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

     Concatenates a fragment of one sequence with a fragment of another
     one.

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

     concat(seqno1=0, seqno2=1, destSeqno=2, from1=1, to1=0, strand1=getStrand(),
     from2=1, to2=0, strand2=getStrand())

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

  seqno1: Integer/scalar, Integer/scalar, First sequence number (buffer
          number)

  seqno2: Integer/scalar, Integer/scalar, Second sequence number
          (buffer number)

destSeqno: Integer/scalar, Output sequence number (buffer number)

 strand1: Integer/scalar, Strand of the first fragment (forward: 0,
          reverse: 1)

from1,to1: Integer/scalar, Absolute addresses of the beginning and the
          end of the first fragment, (1 means the first nucleotide and
          0 conventionally the last one;  from must not be larger than
          to and both vectors must be the same size). 

from2,to2: Integer/scalar, Absolute addresses of the beginning and the
          end of the second fragment, (1 means the first nucleotide and
          0 conventionally the last one;  from must not be larger than
          to and both vectors must be the same size) 

 strand2: Integer/scalar, Strand of the second fragment (forward: 0,
          reverse: 1)

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

     destSeq or -1 if error

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

     L.Cottret

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

     'assemble', 'getSeq',  'appendSeq'

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

     s1<- "aaacgctagcgcg"
     placeString(s1)
     s2<-"ttttctatcag"
     placeString(s2,1)
     concat(seqno1=0,seqno2=1, from1=2,to1=3,from2=8,to2=0, strand1=1)
     getSeq(2)
     #[1] "TTTCAG"
       

