catmap                package:catmap                R Documentation

_c_a_t_m_a_p: _C_a_s_e-_c_o_n_t_r_o_l _A_n_d _T_D_T _M_e_t_a-_A_n_a_l_y_s_i_s _P_a_c_k_a_g_e

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

     'catmap' is an R package that conducts fixed-effects (inverse
     variance) and random-effects (DerSimonian and Laird, 1986)
     meta-analyses of case-control or family-based (TDT) genetic data;
     in addition, it performs meta-analyses combining these two types
     of study designs.  The fixed-effects model was first described by
     Kazeem and Farrall (2005); the random-effects model is described
     in Nicodemus (submitted) and saves a text file to the current
     working directory of all results printed to screen (use getwd() to
     find cwd).

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

     catmapobject<-catmap(dataset, ci, printout) 

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

 dataset: A text file containing a header with the following column
          names: *name, study, t, nt, caserisk, controlrisk,
          casenotrisk, controlnotrisk* in tab-delimited format.  Note
          that the header must be exactly as specified and that all
          cells in the table must have an entry, even if the entry is 0
          or missing (NA).  See for example: data(catmapdata). *The
          dataset argument to catmap should be either the example data
          or a file containing the data for catmap, not an R object.* 

      ci: The confidence level for confidence intervals; 0 < ci < 1. 
          The default is 0.95

printout: Logical.  Should a text file of the fixed- and random-effects
          models and Q statistic results be saved to the current
          working directory?  Output files are saved with the default
          name of *dataset.output.txt* where dataset is the name of the
          file given as the first argument to catmap.  Default = TRUE.

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

     catmap is an R package that conducts fixed-effects (inverse
     variance) and random-effects (DerSimonian and Laird, 1986)
     meta-analyses of case-control or family-based (TDT) genetic data;
     in addition, it performs meta-analyses combining these two types
     of study designs.  The fixed-effects model was first described by
     Kazeem and Farrall (2005); the random-effects model is described
     in Nicodemus (submitted). Cumulative meta-analyses over time and
     leave-one-out sensitivity analyses may be performed using either
     fixed- or random-effects estimates or both estimates may be
     calculated; both produce a .txt file and an optional .pdf plot as
     output. A funnel plot graphic is implemented; however, no formal
     test of publication bias is available (see Ioannidis & Trikalinos,
     2007). If users request a file to be created containing the
     results the file will be saved to the current working directory,
     which users can find by using >getwd(). *Note that a catmap object
     must be created on the first call to catmap. If you do not create
     a catmap object you will not be able to use any of the other
     functions AND you will get a printout of the entire contents to
     screen*

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

     Kristin K. Nicodemus, kristin.nicodemus@well.ox.ac.uk

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

     'catmap.forest', 'catmap.sense', 'catmap.cumulative',
     'catmap.funnel'.

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

     ## Not run: 
     data(catmapdata)        
     catmap(catmapdata, 0.95, TRUE)
     catmapobject1<-catmap(catmapdata, 0.95, TRUE)
     ## End(Not run)

