hg18track-class          package:encoDnaseI          R Documentation

_C_l_a_s_s "_h_g_1_8_t_r_a_c_k" _c_o_n_t_a_i_n_e_r _f_o_r _h_g_1_8 _a_n_n_o_t_a_t_i_o_n
_f_o_u_n_d _i_n _g_e_n_o_m_e _b_r_o_w_s_e_r _t_r_a_c_k _f_i_l_e_s; _c_l_a_s_s "_c_h_r_n_u_m" _e_x_t_e_n_d_s
_n_u_m_e_r_i_c _f_o_r _a_n _i_n_d_e_x_i_n_g _a_p_p_l_i_c_a_t_i_o_n _o_n _h_g_1_8_t_r_a_c_k _o_b_j_e_c_t_s.

_D_e_s_c_r_i_p_t_i_o_n:

     container for hg18 annotation found in genome browser track files

_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("hg18track",
     assayData, featureData, experimentData, annotation, dataVals,
     ...)'. These are single-sample eSet instances.

     Note that 'demoTrk19' is a restriction of the 'rawCD4' structure
     to the interval of chromosome 19 that was assayed in the ENCODE
     project for DnaseI hypersensitivity.

_S_l_o_t_s:


     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"' ~~ 

     '_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"' ~~ 

     '_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': Object of class '"character"' ~~ 

     '.___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 = "hg18track")': select using numeric, logical, or
          chrnum indices. 

     _c_h_r_n_u_m 'signature(object = "hg18track")': extract numeric tokens
          for chromosome number at which data values are obtained; note
          that chrnum is also used as name of a class.

     _d_a_t_a_V_a_l_s 'signature(object = "hg18track")': actual data values 

     _g_e_t_T_r_k_X_Y 'signature(object = "hg18track", type = "character")':
          obtain a list with components x, y indicating location and
          data value respectively; location is within chromosome;
          default type is 'midpoint' of locations given as intervals 

     _g_e_t_T_r_k_X_Y 'signature(object = "hg18track", type = "missing")': 
          take default midpoint x values corresponding to data values 

     _r_a_n_g_e_L_o_c_s 'signature(object = "hg18track")': if measures from only
          one chromosome are present , this returns low and high values
          of chromStart and chromEnd respectively, otherwise error.

     _c_l_i_p_T_r_k 'signature(obj = "hg18track", low="numeric", hi="numeric",
          attr="ANY")': create a restriction of the track using an
          interval specification.  by default the 'chromStart'
          featureData component is used for coordinates to clip; if
          'attr' is non-missing, the featureData component named by
          'attr' will be used.

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "hg18track")': create a new
          instance 

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     showClass("hg18track")
     data(rawCD4)
     rawCD4
     rawCD4.chr1 = rawCD4[ chrnum(1), ]
     rangeLocs(rawCD4.chr1)
     plot(getTrkXY(rawCD4.chr1), ylab="data value", xlab="interval midpt on chr 1" )
     c52 = clipTrk(rawCD4[ chrnum(5), ], 1.30e8, 1.33e8 )
     plot(getTrkXY(c52))

