smlSet-class             package:GGBase             R Documentation

_D_o_c_u_m_e_n_t_a_t_i_o_n _o_n
_S_4 _c_l_a_s_s "_s_m_l_S_e_t" _a_n _e_S_e_t-_d_e_r_i_v_e_d _c_o_n_t_a_i_n_e_r _f_o_r _s_n_p_M_a_t_r_i_x _l_i_s_t_s,
_a_l_l_o_w_i_n_g _e_f_f_i_c_i_e_n_t _c_o_m_b_i_n_a_t_i_o_n _o_f _S_N_P _c_h_i_p _g_e_n_o_t_y_p_i_n_g _w_i_t_h _m_i_c_r_o_a_r_r_a_y
_e_x_p_r_e_s_s_i_o_n _d_a_t_a, _a_n_d _a_l_l_i_e_d _c_l_a_s_s_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Documentation on S4 class "smlSet" an eSet-derived container for
     snpMatrix lists, allowing efficient combination of SNP chip
     genotyping with microarray expression data, and allied classes

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("smlSet",
     assayData, phenoData, featureData, experimentData, annotation,
     ...)'. These objects respond to interrogation on samples,
     expression values, SNP values, and other metadata.

_S_l_o_t_s:


     '_s_m_l_E_n_v': Object of class '"environment"' an environment with
          single key 'smList' pointing to a list of package snpMatrix
          snp.matrix instances 

     '_c_h_r_o_m_I_n_d_s': Object of class '"numeric"' numeric vector indicating
          what chromosomes are represented in the 'smlEnv' 

     '_s_n_p_N_a_m_e_s': Object of class '"character"' list of character
          strings naming SNPs genotyped in smList element of smlEnv 

     '_o_r_g_a_n_i_s_m': Object of class '"character"' informal, "Hs"
          recommended for human 

     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"' intended to hold
          expression data coordinated with the smlEnv data 

     '_p_h_e_n_o_D_a_t_a': Object of class '"AnnotatedDataFrame"'  standard
          sample-level data container from eSet design 

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class '"AnnotatedDataFrame"'  standard
          feature-level metadata container, implied usage is for
          documenting the expresion data elements 

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class '"MIAME"' standard metadata
          container from Biobase eSet design 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' vector giving the
          Bioconductor annotation package (.db type) for decoding
          expression feature identifiers. 

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class '"Versions"' class version
          tracking metadata 

_E_x_t_e_n_d_s:

     Class 'eSet', directly. Class 'VersionedBiobase',  by class
     "eSet", distance 2. Class 'Versioned', by class "eSet",  distance
     3.

_M_e_t_h_o_d_s:


     _s_m_L_i_s_t 'signature(x = "smlSet")': retrieves the actual list of
          snp.matrix entities 

     _s_m_l_E_n_v 'signature(x = "smlSet")': retrieves the environment
          holding snp.matrix entities 

     _e_x_p_r_s 'signature(x = "smlSet")': retrieves the matrix of
          expression values 

     '_c_o_m_b_i_n_e': concatenates expression data and forms intersection of
          SNP sets

     '_g_e_t_A_l_l_e_l_e_s(_s_m_l_S_e_t, _r_s_i_d)': returns A/B notations for SNP
          determined by rsid

_N_o_t_e:

     We have included a '[' method for snp.matrix instances that
     accepts an rsid instance as a column selector.

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_S_e_e _A_l_s_o:

     GGtools package makes extensive use of these classes and methods.

_E_x_a_m_p_l_e_s:

     showClass("smlSet")

