rowlist                package:LMGene                R Documentation

_G_e_n_e _n_a_m_e _l_i_s_t_i_n_g _f_u_n_c_t_i_o_n

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

     This function makes significant gene list for a specified factor,
     where genes are selected as significant by the given p-values and
     significance level.

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

     rowlist(genemat, effnum, apvlist, level, posterior = TRUE)

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

 genemat: A matrix data of array.

  effnum: Factor number.

 apvlist: A vector with FDR adjusted p-value.

   level: Significance level.

posterior: TRUE, if adjusted p-values are to be computed with Posterior
          method.

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

     'genemat' is an n-by-p matrix of expression values.  'effnum' is
     the column number for the effect of interest. 'apvlist' is a
     matrix of p-values from pvadjust or genediff the routine returns a
     list of genes whose FDR p-value is less than level using either
     individual gene or posterior MSE's. This function returns gene
     names if 'rownames(genemat)' is not 'NULL', or gene numbers
     otherwise. 
      'level' indicates False Discovery Rate. e.g.) level 0.05 means 5

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

genelist : A vector containing gene names if 'rownames(genemat)' is not
          'NULL', or gene numbers otherwise.

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

     David Rocke and Geun-Cheol Lee

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

     David M. Rocke (2004), Design and analysis of experiments with
     high throughput biological assay data, Seminars in Cell &
     Developmental Biology, 15, 703-713. 

     <URL: http://www.idav.ucdavis.edu/~dmrocke/>

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

     'LMGene', 'rowaov'

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

     #library
     library(Biobase)
     library(LMGene)

     #data
     data(sample.mat)
     data(vlist)
     LoggedSmpd0<-neweS(lnorm(log(sample.mat)), vlist)

     pvlist <- genediff(LoggedSmpd0)
     apvlist <- pvadjust(pvlist)

     genelist <- rowlist(exprs(LoggedSmpd0), 2, apvlist, 0.01)
     genelist

