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)

