QualityScore-class         package:ShortRead         R Documentation

_Q_u_a_l_i_t_y _s_c_o_r_e_s _f_o_r _s_h_o_r_t _r_e_a_d_s _a_n_d _t_h_e_i_r _a_l_i_g_n_m_e_n_t_s

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

     This class hierarchy represents quality scores for short reads.
     'QualityScore' is a virtual base class, with derived classes
     offering different ways of representing qualities. Methods defined
     on 'QualityScore' are implemented in all derived classes.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects from the class are created using constructors (e.g.,
     'NumericQuality') named after the class name.

_E_x_t_e_n_d_s:

     Class '".ShortReadBase"', directly.

_M_e_t_h_o_d_s:

     The following methods are defined on all 'QualityScore' and
     derived classes:


     [ 'signature(x = "QualityScore", i = "ANY", j = "missing")'

     [ 'signature(x = "MatrixQuality", i = "ANY", j = "missing")':

          Subset the object, with index 'i' indicating the reads for
          which quality scores are to be extracted. The class of the
          result is the same as the class of 'x'. It is an error to
          provide any argument other than 'i'.

     [[ 'signature(x = "QualityScore", i = "ANY", j = "ANY")': 

          Subset the object, returning the quality score (e.g., numeric
          value) of the 'i'th read. 

     [[ 'signature(x = "MatrixQuality", i = "ANY", j = "ANY")':

          Returns the vector of quality scores associated with the
          'i'th read.

     _d_i_m 'signature(x = "MatrixQuality")':

          The integer(2) dimension (e.g., number of reads, read width)
          represented by the quality score.

     _l_e_n_g_t_h 'signature(x = "QualityScore")':

     _l_e_n_g_t_h 'signature(x = "MatrixQuality")':

          The integer(1) length (e.g., number of reads) represented by
          the quality score. Note that 'length' of 'MatrixQuailty' is
          the number of rows of the corresponding matrix, and not the
          length of the corresponding numeric vector.

     _a_p_p_e_n_d 'signature(x = "QualityScore", values = "QualityScore",
          length = "missing")': append 'values' after 'x'.

     _w_i_d_t_h 'signature(x = "QualityScore")':

     _w_i_d_t_h 'signature(x = "NumericQuality")':

     _w_i_d_t_h 'signature(x = "MatrixQuality")':

     _w_i_d_t_h 'signature(x = "FastqQuality")':

          A numeric vector with length equal to the number of quality
          scores, and value equal to the number of quality scores for
          each read. For instance, a 'FastqQuality' will have widths
          equal to the number of nucleotides in the underlying short
          read.


     _s_h_o_w 'signature(object = "QualityScore")':

     _s_h_o_w 'signature(object = "NumericQuality")':

     _s_h_o_w 'signature(object = "FastqQuality")':

          provide a brief summary of the object content.


     _d_e_t_a_i_l 'signature(object = "QualityScore")':

          provide a more detailed view of object content.


     The following methods are defined on specific classes:


     _a_l_p_h_a_b_e_t 'signature(x = "FastqQuality", ...)': Return a character
          vector of valid quality characters.


     _a_l_p_h_a_b_e_t_F_r_e_q_u_e_n_c_y 'signature(stringSet = "FastqQuality")':

          Apply 'alphabetFrequency' to quality scores, returning a
          matrix as described in 'alphabetFrequency'.

     _a_l_p_h_a_b_e_t_B_y_C_y_c_l_e 'signature(stringSet = "FastqQuality")':

          Apply 'alphabetByCycle' to quality scores, returning a matrix
          as described in 'alphabetByCycle'.

     _a_l_p_h_a_b_e_t_S_c_o_r_e 'signature(object = "FastqQuality")':

     _a_l_p_h_a_b_e_t_S_c_o_r_e 'signature(object = "SFastqQuality")':

          Apply 'alphabetScore' (i.e., summed base quality, per read)
          to 'object'.

     _c_o_e_r_c_e 'signature(from = "FastqQuality", to = "numeric")':

     _c_o_e_r_c_e 'signature(from = "FastqQuality", to = "matrix")':

     _c_o_e_r_c_e 'signature(from = "SFastqQuality", to = "matrix")':

          (Use these as, for instance, 'as(from, "matrix")') coerce
          objects of class 'from' to class 'to', using the quality
          encoding implied by the class. WHen 'to' is matrix, the
          result is a matrix of type 'integer'. In addition, methods
          require that all quality scores are of the same width.

     _n_a_r_r_o_w 'signature(x = "FastqQuality", start = NA, end = NA, width
          = NA, use.names = TRUE)': narrow 'qualilty' so that scores
          are between 'start' and 'end' bases, according to 'narrow' in
          the 'IRanges' package.

     _s_r_o_r_d_e_r 'signature(x = "FastqQuality")':

     _s_r_r_a_n_k 'signature(x = "FastqQuality")':

     _s_r_d_u_p_l_i_c_a_t_e_d 'signature(x = "FastqQuality")':

          Apply 'srsort', 'srorder', 'srrank', and 'srduplicated' to
          quality scores, returning objects as described on the
          appropriate help page.


     Integer representations of 'SFastqQuality' and 'FastqQuality' can
     be obtained with 'as(x, "matrix")'.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'NumericQuality' and other constructors.

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

     names(slot(getClass("QualityScore"), "subclasses"))

