accessors             package:ShortRead             R Documentation

_A_c_c_e_s_s_o_r_s _f_o_r _S_h_o_r_t_R_e_a_d _c_l_a_s_s_e_s

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

     These functions are `accessors' (to get and set values) for
     objects in the 'ShortRead' package.

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

     ## SRVector
     vclass(object, ...)
     ## ShortRead / ShortReadQ
     sread(object, ...)
     id(object, ...)
     ## AlignedRead
     chromosome(object, ...)
     position(object, ...)
     alignQuality(object, ...)
     alignData(object, ...)
     ## Solexa
     experimentPath(object, ...)
     dataPath(object, ...)
     scanPath(object, ...)
     imageAnalysisPath(object, ...)
     baseCallPath(object, ...)
     analysisPath(object, ...)
     ## SolexaSet
     solexaPath(object, ...)
     laneDescription(object, ...)
     laneNames(object, ...)

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

  object: An object derived from class 'ShortRead'. See help pages for
          individual objects, e.g., 'ShortReadQ'. The default is to
          extract the contents of a slot of the corresponding name
          (e.g., slot 'sread') from 'object'.

     ...: Additional arguments passed to the accessor. The default
          definitions do not make use of additional arguments.

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

     Usually, the value of the corresponding slot, or other simple
     content described on the help page of 'object'.

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

     Martin Morgan

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

     sp <- SolexaPath(system.file('extdata', package='ShortRead'))
     experimentPath(sp)
     basename(analysisPath(sp))

