plotSnp               package:SNPchip               R Documentation

_P_l_o_t_s _c_o_p_y _n_u_m_b_e_r _a_n_d _g_e_n_o_t_y_p_e _c_a_l_l_s _a_g_a_i_n_s_t _p_h_y_s_i_c_a_l _p_o_s_i_t_i_o_n

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

     Returns an object inheriting from class 'ParESet' - essentially, a
     list of default graphical parameters that can be modified as
     needed. The 'show' method for this class plots the copy number and
     genotype calls versus physical position for an arbitrary number of
     samples and chromosomes.

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

     plotSnp(object, hmmPredict, ...)
     ## S4 method for signature 'SnpLevelSet':
     plot(x, y, ...)

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

object, x: An object extending 'ParESet'

hmmPredict, y: An object of class 'HmmPredict'

     ...: Additional arguments to the initialization methods of the
          'ParESet' classes

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

     See examples in the vignette

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

     R. Scharpf

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

     'par', 'ParESet-class', 'ParSnpCallSet-class',
     'ParSnpCopyNumberSet-class', 'ParSnpSet-class'

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

     data(sample.snpset)
     chr1 <- sample.snpset[chromosome(sample.snpset) == "1", 1]
     graph.par <- plotSnp(chr1)
     class(graph.par)
     ## Not run: 
     graph.par
     ## End(Not run)

