GetSeq                 package:GeneR                 R Documentation

_E_x_t_r_a_c_t _r_e_g_i_o_n_s _f_r_o_m _a _s_e_q_u_e_n_c_e

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

     Return a vector of character string of regions from sequence seqno

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

     multiExtract(seqno=0, comp = getStrand(), from=1, to=0)
     getSeq(seqno=0, comp = getStrand(), from=1, to=0)
     strMultiExtract(s, from=1, to=0)

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

   seqno: Integer, sequence number.  (bufseq)

       s: a sequence (string)

 from,to: Begining and ending of sequence, can be vectors. 0 represent
          the last nucleotide and 1 the first one. 

    comp: Integer. If comp = 1, result will be the complement.

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

     A vector of character string, NULL if error

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

     L.Cottret

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

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

     strMultiExtract(s,from=c(1,5,10),to=c(5,10,15))

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

     ## The reverse complement
     getSeq(0,comp=1) 

