ALICOR              package:encoDnaseI              R Documentation

_a_l_i_g_n_e_d _a_n_d _i_n_t_e_r_p_o_l_a_t_e_d _c_o_r_r_e_l_a_t_i_o_n _f_o_r _l_o_c_a_l
_m_a_x_i_m_u_m _t_r_a_c_e_s _f_o_r _t_w_o _s_c_a_t_t_e_r_p_l_o_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     aligned and interpolated correlation for local maximum traces from
     two scatterplots

_U_s_a_g_e:

     alicor(x1, y1, x2, y2, bin = 50000)
     ALICOR(ssr, dns = rawCD4, bin = 50000)

_A_r_g_u_m_e_n_t_s:

      x1: domain points for first scatterplot

      y1: range points for first scatterplot

      x2: domain points for second scatterplot

      y2: range points for second scatterplot

     ssr: an instance of class 'snpScreenResult' 

     dns: an instance of class 'hg18track' 

     bin: bin size, units are base pairs 

_D_e_t_a_i_l_s:

     We define a scatterplot to be a pair of vectors (x, y). We are
     interested in measuring the distance between two scatterplots,
     focusing on the locations of local peaks and valleys.  Two
     scatterplots are close if their peaks and valleys in y are nearby
     in x.

     We have no restrictions on commonalities between the scatterplots,
     but this only makes sense if there is reasonable overlap between
     their x ranges.

     The algorithm, implemented in low-level function 'alicor', is as
     follows.  Use parameter 'bin' to  define a grid in x for each
     scatterplot, and compute the maximum y value in each x-grid
     interval.  Compute a common domain for the two scatterplots based
     solely on 'x1'. Linearly interpolate the maximal series for each
     scatterplot on the common domain.  Compute the correlation
     coefficient for the resulting interpolated series.

     The higher-level function 'ALICOR' adapts this to
     'snpScreenResult' 'plot_mlp' display data and to hg18 annotation
     track data.

_V_a_l_u_e:

     scalar correlation coefficient

_N_o_t_e:

     Many variations on this algorithm are possible, but the code is
     not very flexible at this time.

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     data(demoPGM1ssr)
     data(demoTrk19)
     ALICOR(demoPGM1ssr,  demoTrk19)

