basecontent           package:matchprobes           R Documentation

_O_b_t_a_i_n _t_h_e _A_T_C_G _c_o_n_t_e_n_t _o_f _a _g_e_n_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function accepts a character vector representing the
     nucleotide sequences and computes the frequencies of each base (A,
     C, G, T).

_U_s_a_g_e:

     basecontent(seq)
     countbases(seq, dna = TRUE)

_A_r_g_u_m_e_n_t_s:

     seq: Character vector.

     dna: Logical value indicating whether the sequence is DNA ('TRUE')
          or RNA ('FALSE')

_D_e_t_a_i_l_s:

     The base frequencies are calculated separately for each element of
     'x'. The elements of 'x' can be in upper case, lower case or
     mixed.

_V_a_l_u_e:

     A matrix with 4 columns and 'length(x)' rows.  The columns are
     named 'A', 'C', 'T', 'G', and the values in each column are the
     counts of the corresponding bases in the elements of 'x'.  When
     'dna=FALSE', the 'T' column is replaced with a 'U' column.

_A_u_t_h_o_r(_s):

     R. Gentleman, W. Huber, S. Falcon

_S_e_e _A_l_s_o:

     'complementSeq','reverseSeq', 'revcompDNA', 'revcompRNA'

_E_x_a_m_p_l_e_s:

      v<-c("AAACT", "GGGTT", "ggAtT")
      basecontent(v)

      countbases(v)