Description Usage Arguments Details Value Author(s) Examples
Given a path/directory (genopath
) that keeps geotype files, phenotype file, pedigree file, phenotype of interest, covariates, analysis of interest
(can be 'lmepack', 'lmepack.imputed', 'lmeVpack.imputed', 'glmm', 'geepack', 'geepack.imputed', 'geepack.quant', 'geepack.quant.imputed', 'lmepack.int', 'lmepack.int.imputed', 'geepack.int', 'geepack.int.imputed',
'geepack.quant.int', 'geepack.quant.int.imputed') and other arguments, auto
function generates one R script, one shell script that can excute
R script, and one list file that can excute all shell scripts in batch mode, for each genotype file. Once the list file (XXXX.lst) is generated,
user can use ksh XXXX.lst to submit all jobs to test all SNPs in genopath
.
1 2 3 |
genopath |
a character string indicating the path/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 |
covars |
a character vector for covariates in |
cov.int |
a character string naming the covariate for interaction, the covariate has to be included in |
sub |
"N" (default) for no stratified analysis, and "Y" for requesting stratified analyses (only when cov.int is dichotomous) |
analysis |
a character string indicating the analysis of interest available in |
lib.loc |
a character string indicating the location of |
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, one shell script that can excute R script, and one list file
that can excute all shell scripts in batch mode. These scripts are named based on the phenotype of interest,
the analysis of interest and the time these scripts are generated. After generating these scripts, auto
function genertates 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, 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>
1 2 3 4 5 6 | ## Not run:
auto(phenfile="simphen.csv",genopath="/home/data/exomechip/chr1",pedfile="simped.csv",
outfile="exomechip_chr1_SIMQT.csv",phen="CVD",covars="sex",analysis="geepack",model="a",
col.names=F,sep.ped=",",sep.phe=",",sep.gen=",")
## End(Not run)
|
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