GenomeDataList-class        package:BSgenome        R Documentation

_L_i_s_t _o_f _G_e_n_o_m_e_D_a_t_a _o_b_j_e_c_t_s

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

     'GenomeDataList' is a list of 'GenomeData' objects. It could be
     useful for storing data on multiple experiments or samples.

_D_e_t_a_i_l_s:

     This is simply an 'AnnotatedList' that requires all of its
     elements to be instances of 'GenomeData'.

     One should try to take advantage of the metadata storage
     facilities provided by 'AnnotatedList'. The 'elementMetadata'
     field, for example, could be used to store the experimental
     design, while the 'metadata' field could store the experimental
     platform.

_C_o_n_s_t_r_u_c_t_o_r:


      'GenomeDataList(elements = list(), metadata = list(),
          elementMetadata = NULL)': Creates a 'GenomeDataList' with the
          elements from the 'elements' parameter, a list of
          'GenomeData' instances. The other arguments correspond to the
          optional metadata stored in 'AnnotatedList'. 


_C_o_e_r_c_i_o_n:


      'as(from, "data.frame")': Coerces each subelement to a data
          frame, and binds them into a single data frame with an
          additional column indicating chromosome


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

     Michael Lawrence

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

     GenomeData, the type of elements stored in this class.
     AnnotatedList, the base of this class.

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

     gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)),
                      organism = "Mmusculus", provider = "UCSC",
                      providerVersion = "mm9")
     gdl <- GenomeDataList(list(gd), elementMetadata = XDataFrame(induced = TRUE))
     gdl[[1]] # get first element

