getFDgene              package:PCpheno              R Documentation

_G_e_t _f_i_t_n_e_s_s _d_e_f_e_c_t _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Function to select genes that present a significant growth defect
     according to the condition(media) or generation time.

_U_s_a_g_e:

     getFDgene(data,condition,cutoff,mode="generation",subset)

_A_r_g_u_m_e_n_t_s:

    data: List of fitness defect scores for genes tested at different
          experimental conditions.

condition: Dataframe of experimental conditions

  cutoff: Numerical vector of length one or more, defining the
          threshold of 'significance' for the fitness defect score

    mode: Character string defining the base of the selection either
          'condition' (media) or 'generation' time, Default=generation.

  subset: Numerical vector or list to which apply the different
          cutoffs.

_V_a_l_u_e:

     Reduced list of gene fitness scores per experimental condition
     according to the experimental condition or the generation time.

_A_u_t_h_o_r(_s):

     N. LeMeur

_R_e_f_e_r_e_n_c_e_s:

     Giaever G. et al. (2002) Functional profiling of the Saccharomyces
     cerevisiae genome. Nature. 418(6896):387-91. PMID: 12140549

_E_x_a_m_p_l_e_s:

      data(GiaeverPheno)
      data(GiaeverExpCdt)
      ##Select all the genes, in the different experimental conditions, that present a fitness score above 20, 100 and 100 at 5, 15 and 20 generations, respectively 
      fitnessGen <- getFDgene(GiaeverPheno,condition=GiaeverExpCdt,cutoff=c(20,100,100),mode="generation",subset=c(5,15,20))
      ##Select all the genes, that present a fitness score above 15 and 100
      ##in the condition set A and B respectively, independently of the generation time 
     fitnessCondt <- getFDgene(GiaeverPheno,condition=GiaeverExpCdt,cutoff=c(100,15),mode="condition",subset=list(a=c(1:23,27,30,31),b=c(24:26,28,29)))

