trackSet-class          package:rtracklayer          R Documentation

_C_l_a_s_s "_t_r_a_c_k_S_e_t"

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

     An object representing a genome annotation track. Based on 'eSet',
     with feature information (chrom, start, end, strand, ...) stored
     in the 'featureData' and data values from experimental
     measurements stored in the 'assayData'.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects of the class are generally created in two different ways,
     depending on how the experimental data are provided. The first way
     is to pass an instance of 'AssayData' as the 'dataVals' parameter
     in 'new("trackSet", assayData, phenoData =
     annotatedDataFrameFrom(assayData, byrow=FALSE), featureData =
     annotatedDataFrameFrom(assayData, byrow=TRUE), experimentData =
     new("MIAME"), annotation = character(), genome = "hg18")'. The
     'AssayData' object must contain a matrix or data.frame named
     'dataVals', which should contain the experimental measurements.
     Alternatively, the experimental measurements may be passed as the
     'dataVals' parameter in 'new("trackSet", phenoData =
     annotatedDataFrameFrom(assayData, byrow=FALSE), featureData =
     annotatedDataFrameFrom(assayData, byrow=TRUE), experimentData =
     new("MIAME"), annotation = character(), dataVals = matrix(),
     genome = "hg18")'.

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


     '_g_e_n_o_m_e': Object of class '"character"' identifying the genome to
          which this track pertains. Should be specified according to
          the conventions of the UCSC browser (e.g. "hg18"), if
          possible.

     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"' holding the
          experimental measurements. 

     '_p_h_e_n_o_D_a_t_a': Object of class '"AnnotatedDataFrame"' holding the
          experimental design matrix. 

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class '"AnnotatedDataFrame"' holding the
          feature information, generally including columns 'chrom'
          (chromosome name), 'start' (numeric start position), 'end'
          (numeric end position) and 'strand' (DNA strand: "+", "-" or
          'NA'). Note that the intervals are closed, i.e. the selected
          region is [start,stop].

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class '"MIAME"' with experimental
          metadata. 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' identifying the
          annotation resource. 

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

_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:


     '_o_b_j_e_c_t[_i, _j]' Subsets an instance, where 'i' is an feature index,
          feature name or 'chrid' for selecting features and 'j' is a
          sample index or name for selecting samples from the
          experimental data.

     '_c_h_r_i_d(_o_b_j_e_c_t)' Obtains an instance of 'chrid', which is a vector
          with an element representing the chromosome for each feature
          in this track. 

     '_d_a_t_a_V_a_l_s(_o_b_j_e_c_t)' Retrieves the matrix containing the
          experimental data values.

     '_c_h_r_o_m(_o_b_j_e_c_t)' Retrieves the chromosome identifiers of the
          features. 

     '_s_t_a_r_t(_x)' Retrieves the start positions of the features. 

     '_e_n_d(_x)' Retrieves the end positions of the features. Note that
          intervals are closed, so this should be the index of the last
          base to include in the feature.

     '_s_t_r_a_n_d(_o_b_j_e_c_t)' Retrieves the strand ("+", "-" or 'NA') of the
          features. 

     '_g_e_n_o_m_e_S_e_g_m_e_n_t(_o_b_j_e_c_t)' obtain the genome segment spanned by this
          track (including gaps). 

     '_t_r_a_c_k_D_a_t_a(_o_b_j_e_c_t)' Obtain a representation of this track as a
          'data.frame'. The result is the column-wise combination of
          the 'featureData' slot with the 'dataVals' matrix. The
          function also adds a 'seqMid' column, which holds the
          mid-point of the segment of each feature. This is useful for
          e.g. plotting.

     '_g_e_n_o_m_e(_o_b_j_e_c_t)' Get the 'genome' slot.

     _a_s(_t_r_a_c_k_S_e_t, "_d_a_t_a._f_r_a_m_e") Equivalent to 'trackData' above.

     '_t_r_a_c_k_S_e_t_s(_o_b_j_e_c_t)' Create a 'trackSets' instance initially
          containing only this track. 

     '_e_x_p_o_r_t._b_e_d(_o_b_j_e_c_t, _c_o_n, _w_i_g = _F_A_L_S_E)' Export track in Browser
          Extended Display (BED) format. 

     '_e_x_p_o_r_t._g_f_f(_o_b_j_e_c_t, _c_o_n,         _v_e_r_s_i_o_n = _c("_1", "_2", "_3"), _s_o_u_r_c_e = "_r_t_r_a_c_k_l_a_y_e_r")' 
          Export track in General Feature Format (GFF). 

     '_e_x_p_o_r_t._u_c_s_c(_o_b_j_e_c_t, _c_o_n, _s_u_b_f_o_r_m_a_t = _c("_g_f_f", "_w_i_g"),         _n_a_m_e = _d_e_p_a_r_s_e(_s_u_b_s_t_i_t_u_t_e(_o_b_j_e_c_t)), ...)' 
          Export track in the meta format of the (UCSC) browser. 

     '_e_x_p_o_r_t._w_i_g(_o_b_j_e_c_t, _c_o_n,         _d_a_t_a_F_o_r_m_a_t = _c("_b_e_d", "_v_a_r_i_a_b_l_e_S_t_e_p", "_f_i_x_e_d_S_t_e_p"))' 
          export track in Wiggle (WIG) format. 

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

     Michael Lawrence

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

     'layTrack' for loading a track into a genome browser. 'import' to
     create a 'trackSet' from a file, 'export' to write a 'trackSet' to
     a file.

