smlSet-class             package:GGtools             R Documentation

_C_l_a_s_s "_s_m_l_S_e_t" - _e_f_f_i_c_i_e_n_t _r_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _S_N_P+_e_x_p_r_e_s_s_i_o_n _d_a_t_a,
_b_a_s_e_d _o_n _C_l_a_y_t_o_n _s_n_p_M_a_t_r_i_x _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Efficient representation of SNP+expression data, based on Clayton
     snpMatrix package.  Supports efficient subsetting of whole-genome
     snp genotyping by chromosome.

_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", smlEnv,
     assayData, phenoData, featureData, experimentData, annotation,
     ...)'.

_S_l_o_t_s:


     '_s_m_l_E_n_v': Object of class '"environment"' - there is one key
          'smList' with value a list of 'snp.matrix' from snpMatrix
          package 

     '_s_n_p_L_o_c_P_a_t_h_M_a_k_e_r': OBSOLETE - IGNORE

     '_c_h_r_o_m_I_n_d_s': Object of class '"numeric"', a numeric vector telling
          what chromosomes are represented. If chromosomes 20 and 21
          are present, the values is c(20,21).  X and Y are 23, 24.

     '_o_r_g_a_n_i_s_m': Object of class '"character"'; string such as Hs for
          modern humans. 

     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"'; container for
          expression data as in ExpressionSet 

     '_p_h_e_n_o_D_a_t_a': Object of class '"AnnotatedDataFrame"'; container for
          sample data as in ExpressionSet  

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class '"AnnotatedDataFrame"'; container
          for expression feature data as in ExpressionSet

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class '"MIAME"'; container for MIAME
          schema  

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"'; vector with names
          'exprs' and 'snps'; 'exprs' should be the name of a
          SQLite-based Bioconductor annotation package  

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class '"Versions"' ~~ 

_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:


     [ 'signature(x = "smlSet")': subsetting must be done with care.
          The usual idiom is 'X[G, S]' where 'G' restricts reporters
          and 'S' restricts samples.  Reporter restriction: At present
          one can use an instance of 'chrnum' class to obtain a
          subsetted object with SNP data restricted to specified
          chromosomes. Sample restriction: works in the customary way
          for 'eSet' instances. 

     _e_x_p_r_s 'signature(object = "smlSet")': return the expression data
          matrix. 

     _g_w_S_n_p_S_c_r_e_e_n 'signature(sym = "genesym", sms = "smlSet")': Execute
          snpMatrix snp.rhs.tests for all SNP in the genome.  Returns
          instance of gwSnpScreenResult. 

     _c_w_S_n_p_S_c_r_e_e_n 'signature(sym = "genesym", sms = "smlSet",
          cnum="chrnum")': Execute snpMatrix snp.rhs.tests for all SNP
          on the specific chromosome.  Returns instance of
          cwSnpScreenResult. 

     _n_s_a_m_p 'signature(x = "smlSet")': returns number of samples. 

     _r_a_w_S_N_P 'signature(x = "smlSet", chrind = "numeric")': returns byte
          (raw) representation of SNP data in snp.matrix format for
          specified chromosome.  

     _g_e_t_S_n_p_L_o_c_s 'signature(x = "smlSet")': returns all relevant
          locations in order of rs numbers in the snp.matrices as a
          single vector

     _g_e_t_S_n_p_C_h_r_o_m_s 'signature(x = "smlSet")': returns all relevant
          chromosome assignments in order of rs numbers in the
          snp.matrices as a single vector

     _s_a_m_p_l_e_N_a_m_e_s 'signature(object = "smlSet")': returns vector of
          sample names. 

     _s_h_o_w 'signature(object = "smlSet")': prints short report. 

     _s_m_L_i_s_t 'signature(x = "smlSet")': returns the list of snp.matrix
          encoding genotypes. 

     _s_m_l_E_n_v 'signature(x = "smlSet")': returns the environment in which
          the smList list is contained. 

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     #showClass("smlSet")
     data(hmceuB36.2021)
     rawSNP(hmceuB36.2021, 20)[1:5,1:5]
     exprs(hmceuB36.2021)[1:5,1:5]

