getRelSignStrength        package:splicegear        R Documentation

_f_u_n_c_t_i_o_n_s _t_o _p_e_r_f_o_r_m _S_P_L_I_C_E

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

     Implementations of the SPLICE algorithm

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

     getRelSignStrength(x, tissue = as.factor(1:ncol(x)), fun = mean, nipt = 30, nitt = 30, ...)

     getFinalRatio(x, tissue=as.factor(1:ncol(x)), fun=mean, ...)

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

       x: a matrix. One probe per line, one column per sample.
          Typically this would be the slot 'exprs' of an instance of
          class 'ExprSet'.

  tissue: a covariate (factor) about the samples.

     fun: a function to obtain a summary value ('mean' by default) 

    nipt: see reference. 

    nitt: see reference. 

     ...: optional parameters for the function 'fun' 

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

     'getFinalRatio' will call 'getRelSignStrength'. The values are
     log-transformed. It is probably a good idea to avoid feeding
     function with values that are already on log scale.

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

     A matrix of the same dimension than the input 'x', holding 'RSS'
     (Relative Signal Strength) or 'final ratios' respectively, as
     described in the reference. Two attributes 'nip' and 'nit' are
     attached the returned matrix.

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

     laurent@cbs.dtu.dk

_R_e_f_e_r_e_n_c_e_s:

     Genome Research (2001), Hu et. al., vol. 11, p.1244

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

     data(spliceset)

     ## The intensity values in the example are log-transformed.
     ## Undo by taking the exponential
     exprs(spliceset) <- exp(exprs(spliceset))

     ## Re-order the rows of different slots to have the probes sorted by
     ## position
     spliceset <- sort.SpliceExprSet(spliceset)
     ## extract the expression matrix
     expr.m <- exprs(spliceset)
     fr <- getFinalRatio(expr.m, tissue=pData(spliceset@eset)[[1]])

