AnnotatedSnpSet-class        package:SNPchip        R Documentation

_C_l_a_s_s "_A_n_n_o_t_a_t_e_d_S_n_p_S_e_t"

_D_e_s_c_r_i_p_t_i_o_n:

     Container for genotype and copy number data from SNP chips, as
     well as chromosome-level features

_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("AnnotatedSnpSet", phenoData, assayData, experimentData,
     featureData, annotation, chromosomeAnnotation)'.

_S_l_o_t_s:

     '_c_h_r_o_m_o_s_o_m_e_A_n_n_o_t_a_t_i_o_n': Object of class 'data.frame' containing
          chromosome-level annotation 

     '_a_s_s_a_y_D_a_t_a': Object of class 'AssayData' containing copy number
          and genotype call matrices 

     '_p_h_e_n_o_D_a_t_a': Object of class 'AnnotatedDataFrame'  

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class 'AnnotatedDataFrame'.  Contains
          annotation for the SNP's, such as chromosome, physical
          position, and alleles. 

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class 'MIAME'  

     '_a_n_n_o_t_a_t_i_o_n': Character string for type of SNP chip. e.g.,
          "pd.mapping50k.xba240"

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class 'Versions'  

_E_x_t_e_n_d_s:

     Class 'AnnotatedSnpCallSet', directly. Class
     'AnnotatedSnpCopyNumberSet', directly. Class 'SnpCallSet', by
     class AnnotatedSnpCallSet, distance 2. Class 'eSet', by class
     AnnotatedSnpCallSet, distance 3. Class 'VersionedBiobase', by
     class AnnotatedSnpCallSet, distance 4. Class 'Versioned', by class
     AnnotatedSnpCallSet, distance 5. Class 'SnpCopyNumberSet', by
     class AnnotatedSnpCopyNumberSet, distance 2. Class 'eSet', by
     class AnnotatedSnpCopyNumberSet, distance 3. Class
     'VersionedBiobase', by class AnnotatedSnpCopyNumberSet, distance
     4. Class 'Versioned', by class AnnotatedSnpCopyNumberSet, distance
     5.

_M_e_t_h_o_d_s:

     _a_l_l_e_l_e_A 'signature(object="AnnotatedSnpSet")': return the A allele
          for the specified SNPs in object

     _a_l_l_e_l_e_B 'signature(object="AnnotatedSnpSet")': return the B allele
          for the specified SNPs in object

     _c_h_r_o_m_o_s_o_m_e 'signature(object="AnnotatedSnpSet")': accessor for the
          chromosome

     _f_D_a_t_a 'signature(object="AnnotatedSnpSet")': accessor for the
          data.frame containing feature-level annotation. Usually very
          large.    

     _f_r_a_g_m_e_n_t_L_e_n_g_t_h 'signature(object="AnnotatedSnpSet")': accessor for
          the length of the PCR fragment on which the SNP resides    

     _p_l_o_t_C_y_t_o_b_a_n_d 'signature(object="AnnotatedSnpSet")': Plots the
          cytoband for a single chromosome.

     _p_l_o_t_S_n_p 'signature(object="AnnotatedSnpSet", ...)': Makes a
          scatterplot of copy number (vertical axis) versus physical
          position (horizontal axis) for each chromosome and sample in
          the AnnotatedSnpSet object.  Points are color-coded by the
          genotype call.

     _p_o_s_i_t_i_o_n 'signature(object="AnnotatedSnpSet")': Returns physical
          position of SNP along the chromosome in numbers of basepairs
          from the 5' end (an integer)

_N_o_t_e:

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

     Rob Scharpf

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

_S_e_e _A_l_s_o:

     'plotSnp'

_E_x_a_m_p_l_e_s:

     data(annSnpset)
     annSnpset
     ##for formatting the plot layout, see the vignette
     plotSnp(annSnpset, 1:10, 1:2)

