Description Usage Arguments Details Value Author(s) Examples
Fit logistic regression via Generalized Estimation Equation (GEE) to test associations between a dichotomous phenotype
and all imputed SNPs in a genotype file in family data under additive genetic model. Each family is treated as
a cluster, with independence working correlation matrix used in the robust variance estimator.
This function applies the same trait-SNP association test to all SNPs in the imputed genotype data.
The trait-SNP association test is carried out by geepack.lgst.imputed
function where the
geese
function from package geepack
is used.
1 2 | geepack.lgst.batch.imputed(genfile, phenfile, pedfile, outfile, phen,
covars = NULL, col.names = T, sep.ped = ",", sep.phe = ",", sep.gen = ",")
|
genfile |
a character string naming the genotype file for reading (see format requirement in details) |
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 |
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 |
Similar to the details for geepack.lgst.batch
but here the SNP data contains imputed genotypes (allele dosages)
that are continuous and range from 0 to 2. In addition, the user-specified genetic model argument is not available.
No value is returned. Instead, results are written to outfile
.
phen |
phenotype name |
snp |
SNP name |
N |
the number of individuals in analysis |
Nd |
the number of individuals in affected sample in analysis |
AF |
imputed allele frequency of coded allele |
AFd |
imputed allele frequency of coded allele in affected sample |
beta |
regression coefficient of SNP covariate |
se |
standard error of |
remark |
warning or additional information for the analysis, note that the genotype counts are based on rounded imputed genotypes; 'not converged' indicates the GEE analysis did not converge; 'logistic reg' indicates GEE model is replaced by logistic regression; 'exp count<5' indicates any expected count is less than 5 in phenotype-genotype table; 'not converged and exp count<5', 'logistic reg & exp count<5' are noted similarly; 'collinearity' indicates collinearity exists between SNP and some covariates |
pval |
p-value of the association test based on chi-square statistic |
Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>
1 2 3 4 5 6 | ## Not run:
geepack.lgst.batch.imputed(phenfile="simphen.csv",genfile="simgen.csv",
pedfile="simped.csv",phen="aff",covars="sex",outfile="simout.csv",col.names=T,
sep.ped=",",sep.phe=",",sep.gen=",")
## End(Not run)
|
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