getSeq                 package:GeneR                 R Documentation

_S_e_q_u_e_n_c_e _f_r_a_g_m_e_n_t_s _e_x_t_r_a_c_t_i_o_n

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

     Extracts sequence fragments. getSeq further converts the fragments
     in character strings from the GeneR sequence buffer.

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

     getSeq(seqno=0, strand = getStrand(), from=1, to=0)

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

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

from, to: Integer/scalar, Absolute addresses of the begin and the end
          of the 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)

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

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

     A vector of character strings. if error : NULL

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

     L.Cottret

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

     'assemble', 'concat', 'appendSeq', and for character string
     manipulation: 'substr'

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

     s<-"cgtagtagctagctagctagctagctag"
     placeString (s, seqno=1)
     getSeq(1,from=c(1,5,10),to=c(5,10,15))
     #[1] "CGTAG"  "GTAGCT" "TAGCTA"

     # And on the reverse:
     setStrand(1)
     getSeq(1,from=c(1,5,10),to=c(5,10,15))

     ## The reverse complement
     getSeq(1,strand=1) 

