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 coumn 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 returs 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(LoggedSmpd0@exprs,2,apvlist,0.01)
     genelist

