QualityScore            package:ShortRead            R Documentation

_C_o_n_s_t_r_u_c_t _o_b_j_e_c_t_s _i_n_d_i_c_a_t_i_n_g _r_e_a_d _o_r _a_l_i_g_n_m_e_n_t _q_u_a_l_i_t_y

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

     Use these functions to construct quality indicators for reads or
     alignments. See 'QualityScore' for details of object content and
     methods available for manipulating them.

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

     NumericQuality(quality = numeric(0))
     IntegerQuality(quality = integer(0))
     MatrixQuality(quality = new("matrix"))
     FastqQuality(quality, ...)
     SFastqQuality(quality, ...)

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

 quality: An object used to initialize the data structure. Appropriate
          objects are indicated in the constructors above for Numeric,
          Integer, and Matrix qualities. For 'FastqQuality' and
          'SFastqQuality', methods are defined for 'BStringSet',
          'character', and 'missing'.

     ...: Additional arguments, currently unused.

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

     Constructors return objects of the corresponding class derived
     from 'QualityScore'.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'QualityScore', 'readFastq', 'readAligned'

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

     nq <- NumericQuality(rnorm(20))
     nq
     quality(nq)
     quality(nq[10:1])

