assemble                package:GeneR                R Documentation

_C_o_n_c_a_t_e_n_a_t_e_s _p_a_r_t_s _o_f _a _s_e_q_u_e_n_c_e

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

     concatenates parts of a sequence (in any strand) and puts
     resulting sequence in destination sequence buffer.

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

     assemble(seqno=0, from=1, to=0, strand=getStrand(), destSeqno=1)

_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)

  strand: Integer/vector, Strand (forward: 0, reverse: 1)

destSeqno: Output sequence number

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

     destSeqno or -1 if error.

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

     L.Cottret

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

     'getSeq', 'concat' ,'appendSeq'

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

     s<-"aaaacgtagctagctagctacccccctagctacgtagattttt"
     placeString(s)
     x<-c(1,21,39)
     y<-c(4,28,0)
     assemble(from=x,to=y)
     assemble(from=x,to=y,strand=c(0,1,0),destSeqno=2)
     getSeq(1)
     getSeq(2)

