LocalFDR               package:anapuce               R Documentation

_L_o_c_a_l _F_D_R

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

     Estimation of local false discovery rates

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

     LocalFDR(dataf = dataf, graph = TRUE, method = NULL, lambda0 = 0.5, smoothing = "1", thres = c(0.01, 0.05, 0.1, 0.2), mm = c(3, 5, 15, NA))

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

dataf       : input data file with two columns (1 = gene name, 2=
          ordered raw pvalues). 

graph       : if TRUE a pdf graphic is created.

method      : method for estimating m0. This must be one of the strings
          "adaptive", "conservative", "bootstap", "smoother" or NULL. 

lambda0     : value used in calculating m0. 

smoothing   : "1" for the initial published method, "2" for the PAVA
          method isotonic (monotonely increasing nonparametric) least
          squares regression - see P. Broberg (2005). 

thres       : threshold defining intervals used for the movering
          average smoothing. 

mm          : parameter defining intervals used for the movering
          average smoothing. 

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

     - if graph = TRUE, a file of graphics named LocalFDRGraph.pdf

     - A data file (LocalFDRFile.txt) with 4 columns : gene name, raw
     pvalues and two columns corresponding to smoothed FDR values.

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

     J. Aubert

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

     Aubert J, Bar-Hen A, Daudin J.J, Robin S (2004) Determination of
     the differentially expressed genes in microarrays experiments
     using local FDR, _BMC Bioinformatics_, *5:125*.

     Aubert J , Bar-Hen A, Daudin J.J, Robin S (2005) Correction:
     Determination of the differentially expressed genes in microarray
     experiments using local FDR, _BMC Bioinformatics_, *6:42*.

     Per Broberg (2005) A comparative review of estimates of the
     proportion unchanged genes and the false discovery rate, _BMC
     Bioinformatics_ *6:199*

