auto {GWAF} | R Documentation |
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.
auto(genopath, phenfile, pedfile, outfile, phen, covars = NULL, analysis, lib.loc, model = NULL, kinmat = NULL, col.names = F, sep.ped = ",", sep.phe = ",", sep.gen = ",")
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 |
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.
No value is returned. Instead, results are written to outfile
.
Ming-Huei Chen <mhchen@bu.edu> and Qiong Yang <qyang@bu.edu>