auto                  package:GWAF                  R Documentation

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

     Given a phenotype file, a pedigree file, a phenotype of interest,
     covariates, analysis of interest (can be 'lme', 'lme.imputed',
     'gee' or 'gee.imputed'), a path or directory ('genopath') that
     keeps geotype files,  and other arguments, 'auto' function
     generates one R script and one shell script that excutes the R
     script for each genotype file, and one list file that excutes all
     shell scripts in batch mode.

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

     auto(genopath, phenfile, pedfile, outfile, phen, covars = NULL, analysis, lib.loc, model = NULL, 
     kinmat = NULL, col.names = F, sep.ped = ",", sep.phe = ",", sep.gen = ",")

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

genopath: a character string indicating the path or directory that
          keeps genotype files to be analyzed 

phenfile: a character string naming the phenotype file for reading (see
          format requirement in details) 

 pedfile: a character string naming the pedigree file for reading (see
          format requirement in details) 

 outfile: a character string naming the result file for writing 

    phen: a character string for a phenotype name in phenfile 

  covars: a character vector for covariates in phenfile 

analysis: a character string indicating the analysis of interest
          available in 'GWAF' package, can be 'lme', 'lme.imputed',
          'gee' or 'gee.imputed' 

 lib.loc: a character string indicating the location of 'GWAF' package 

   model: a single character of 'a','d','g', or 'r', with 'a'=additive,
          'd'=dominant, 'g'=general and 'r'=recessive models; Not
          appropriate/needed for analyzing imputed SNPs 

  kinmat: a character string naming the file where kinship coefficient
          matrix is kept; needed for LME analyses 

col.names: a logical value indicating whether the output file should
          contain column names 

 sep.ped: the field separator character for pedigree file 

 sep.phe: the field separator character for phenotype file 

 sep.gen: the field separator character for genotype file 

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

     'auto' function generates one R script and one shell script that
     excutes the R script for each genotype file, and one list file 
     that can excute all shell scripts in batch mode to analyze all
     genotype data in 'genopath'. These scripts are named based on the
     phenotype of interest, the analysis of interest and the time these
     scripts are generated. After creating these scripts, 'auto' 
     function gives a message telling the user how to submit ALL the
     jobs (using ksh XXXX.lst). When a submitted job is completed, a
     log file indicating which genotype file was analyzed will be
     generated and the R script and the  shell script will be removed.
     The number of log files should equal to the number of genotype
     files in 'genopath', if all jobs  are completed. All the results
     will be written and appended to the user specified single output
     file. Different 'outfile' should be assigned for different
     'genopath' to avoid over-writting.

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

     No value is returned. Instead, results are written to 'outfile'.

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

     Ming-Huei Chen <mhchen@bu.edu> and Qiong Yang <qyang@bu.edu>

