ALICOR              package:encoDnaseI              R Documentation

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_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)

