Isoqqstat              package:IsoGene              R Documentation

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

     The function calculates SAM test statistics from permutations for
     the five test statistics (the global likelihood test, Williams,
     Marcus, M, and the modified M).

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

       Isoqqstat(x, y, fudge, niter)

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

       x: indicates the dose levels

       y: gene expression for all genes

   fudge: the fudge factor value to be used in the SAM test statistics:
          either fudge="pooled" then it is calculated by the function,
          or fudge="none" then no fudge factor is used

   niter: number of permutations used in the SAM procedure

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

     A list with components 

     aa1: the matrix of the observed test statistic values using the
          likelihood ratio test with 4 columns: the first column
          contains the  observed test statistic values sorted in
          ascending order, the second contains the mean expected test
          statistic values obtained from permutations, the third column
          contains the difference between the first and the second
          column, and the last column gives the ranking of the genes in
           ascending order.

     to1: the matrix of the test statistic values from permutations
          using the likelihood ratio test: each column of the matrix
          corresponds to the sorted test statistic from each
          permutation in an ascending order.

     aa2: the matrix of the observed test statistic values using
          Williams' test with 4 columns: the first column is the sorted
          observed test statistic values in an ascending order, the
          second is the mean expected test statistic values obtained
          from permutations, the third column is the difference between
          the first and the second column, and the last column is the
          rankings of the genes in an ascending order.

     to2: the matrix of the test statistic values from permutations
          using Williams' test: each column of the matrix corresponds
          to the sorted test statistic from each permutation in an
          ascending order.

     aa3: the matrix of the observed test statistic values using
          Marcus' test with 4 columns: the first column is the sorted
          observed test statistic values in an ascending order, the
          second is the mean expected test statistic values obtained
          from permutations, the third column is the difference between
          the first and the second column, and the last column is the
          rankings of the genes in an ascending order.

     to3: the matrix of the test statistic values from permutations
          using Marcus' test: each column of the matrix corresponds to
          the sorted test statistic from each permutation in an
          ascending order.

     aa4: the matrix of the observed test statistic values using the M
          test with 4 columns: the first column is the sorted observed
          test statistic values in an ascending order, the second is
          the mean expected test statistic values obtained from
          permutations, the third column is the difference between the
          first and the second column, and the last column is the
          rankings of the genes in an ascending order.

     to4: the matrix of the test statistic values from permutations
          using the M test: each column of the matrix corresponds to
          the sorted test statistic from each permutation in an
          ascending order.

     aa5: the matrix of the observed test statistic values using the
          modified M test with 4 columns: the first column is the
          sorted observed test statistic values in an ascending order,
          the second is the mean expected test statistic values
          obtained from permutations, the third column is the
          difference between the first and the second column, and the
          last column is the rankings of the genes in an ascending
          order.

     to5: the matrix of the test statistic values from permutations
          using the modified M test: each column of the matrix
          corresponds to the sorted test statistic from each
          permutation in an ascending order.

_N_o_t_e:

     This function calculates the SAM test statistics to be used in the
     SAM procedure for the five test statistics. To use the SAM
     procedure, the number of genes in the data set is preferably
     larger than 500.

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

     Lin et al.

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

     'isoreg', 'Isoallfdr', 'IsoGenemSAM'
     'Isoqval','IsoTestSAM','IsoSAMPlot'

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

       set.seed(1234)
       x <- c(rep(1,3), rep(2,3), rep(3,3))
       y1 <- matrix(rnorm(9000, 1,1), 1000, 9)   # 1000 genes with no trends
       y2 <- matrix(c(rnorm(3000, 1,1), rnorm(3000,2,1), rnorm(3000,3,1)),
                    1000, 9)  # 1000 genes with increasing trends
       y <- data.frame(rbind(y1, y2))  # y needs to be a data frame
       qqstat <- Isoqqstat(x, y, fudge="pooled", niter = 100)

