compute.gc               package:Ringo               R Documentation

_C_o_m_p_u_t_e _t_h_e _G_C _c_o_n_t_e_n_t _o_f _D_N_A _a_n_d _p_r_o_b_e _s_e_q_u_e_n_c_e_s

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

     Simple auxiliary function to compute the GC content of a given set
     of DNA sequences, such as microarray probe sequences.

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

     compute.gc(probe.sequences, digits = 2)

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

probe.sequences: character vector of DNA or probe sequences of which
          the GC content is to be computed

  digits: integer specifying the desired precision

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

     a numeric vector with sequence-wise GC contents; the names of this
     vector are the names of the supplied 'probe.sequences'.

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

     Joern Toedling

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

     Function 'basecontent' in package 'matchprobes' for a more general
     function to compute base occurrence in sequences

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

       ex.seqs <- c("gattaca", "GGGNTT", "ggAtT", "tata","gcccg")
       names(ex.seqs) <- paste("sequence",1:5,sep="")
       compute.gc(ex.seqs)

