locusLevelData          package:VanillaICE          R Documentation

_B_a_s_i_c _d_a_t_a _e_l_e_m_e_n_t_s _r_e_q_u_i_r_e_d _f_o_r _t_h_e _H_M_M

_D_e_s_c_r_i_p_t_i_o_n:

     This object is a list containing the basic data elements required
     for the HMM

_U_s_a_g_e:

     data(locusLevelData)

_F_o_r_m_a_t:

     A list

_D_e_t_a_i_l_s:

     The basic assay data elements that can be used for fitting the HMM
     are:

     1.  a mapping of platform identifiers to chromosome and physical
     position

     2. (optional) a matrix of copy number estimates

     3. (optional) a matrix of confidence scores for the copy number
     estimates (e.g., inverse standard deviations)

     4. (optional) a matrix of genotype calls

     5. (optional) CRLMM confidence scores for the genotype calls

     At least (2) or (4) is required.  The locusLevelData is a list
     that contains (1), (2), (4), and (5).

_S_o_u_r_c_e:

     A HapMap sample on the Affymetrix 50k platform.  Chromosomal
     alterations were simulated.  The last 100 SNPs on chromosome 2
     are, in fact, a repeat of the first 100 SNPs on chromosome 1 -
     this was added for internal use.

_E_x_a_m_p_l_e_s:

     data(locusLevelData)
     str(locusLevelData)

