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)

