XStringQuality-class       package:Biostrings       R Documentation

_P_h_r_e_d_Q_u_a_l_i_t_y _a_n_d _S_o_l_e_x_a_Q_u_a_l_i_t_y _o_b_j_e_c_t_s

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

     Objects for storing string quality measures.

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

       ## Constructors:
       PhredQuality(x)
       SolexaQuality(x)

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

       x: Either a character vector, BString, BStringSet, integer
          vector, or number vector of error probabilities. 

_D_e_t_a_i_l_s:

     'PhredQuality' objects store characters that are interpreted as [0
     - 99] quality measures by subtracting 33 from their ASCII decimal
     representation (e.g. ! = 0, " = 1, # = 2, ...).

     'SolexaQuality' objects store characters are interpreted as [-5 -
     99] quality measures by subtracting 64 from their ASCII decimal
     representation (e.g. ; = -5, < = -4, = = -3, ...).

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

     P. Aboyoun

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

     'pairwiseAlignment', PairwiseAlignedXStringSet-class,
     DNAString-class, BStringSet-class

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

       PhredQuality(0:40)
       SolexaQuality(0:40)

       PhredQuality(seq(1e-4,0.5,length=10))
       SolexaQuality(seq(1e-4,0.5,length=10))

