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:

     Plots copy number and genotype call versus physical position for
     an arbitrary number of samples and chromosomes.

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

     plotSnp(object, snpset, ...)

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

  object: An object extending 'ParESet'

  snpset: An object extending 'SnpLevelSet'

     ...: Arguments to par

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

     See examples in the vignette

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

_N_o_t_e:

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

_R_e_f_e_r_e_n_c_e_s:

_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 <- getPar(chr1, use.chromosome.size=TRUE)
     plotSnp(graph.par, chr1)

