autocor                package:Ringo                R Documentation

_F_u_n_c_t_i_o_n _t_o _c_o_m_p_u_t_e _a_u_t_o-_c_o_r_r_e_l_a_t_i_o_n _o_f _p_r_o_b_e _i_n_t_e_n_s_i_t_i_e_s

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

     Function to compute auto-correlation of probe intensities at
     specified offsets from the original positions.

_U_s_a_g_e:

     autocor(x, probeAnno, chrom = "1", samples = NULL, lag.max = 2000,
     lag.step=100, cor.method = "pearson", 
     channel = c("red","green","logratio"), verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

       x: an object either of class 'ExpressionSet' containing the
          normalized probe intensities or of class 'RGList' containing
          the raw intensities.

probeAnno: Environment holding chromosomal start positions and indices
          of probes in data matrix.

   chrom: character; chromosome to compute the autocorrelation for

 samples: which samples of the data to use; if more than 1 for each
          probe the mean intensity over these samples is taken.

 lag.max: integer; maximal offset from the original position, the
          auto-correlation is to be computed for.

lag.step: integer; step size of lags between 0 and maximal lag.

cor.method: character; which type of correlation to compute, translates
          to argument 'method' of function 'cor'

 channel: character; in case 'x' is an 'RGList', which channel to plot,
          either 'red', 'green' or the 'logratio'
          'log2(red)-log2(green)'

 verbose: logical; extended output to STDOUT

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

     the lags, i.e. the offsets from the original position, the
     auto-correlation is to be computed for, are constructed from the
     given arguments as 'seq(0, lag.max, by=lag.step)'.

_V_a_l_u_e:

     Object of class 'autocor.result', a numeric vector of
     auto-correlation values at the offsets specified in argument
     'lags'. The lag values are stored as the 'names' of the vector.
     Argument 'chrom' is stored as attribute 'chromosome' of the
     result.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'cor','plot.autocor.result'

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

       exDir <- system.file("exData",package="Ringo")
       load(file.path(exDir,"exampleProbeAnno.rda"))
       load(file.path(exDir,"exampleX.rda"))
       exAc <- autocor(exampleX, probeAnno=exProbeAnno,
                       chrom="9", lag.max=1000)
       plot(exAc)

