gee.lgst.batch.imputed {GWAF} | R Documentation |
Fit logistic regression via GEE to test association between a dichotomous phenotype
and all imputed SNPs in a genotype file. 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 gee.lgst function where the
the gee()
function from package gee
is used.
gee.lgst.batch.imputed(genfile, phenfile, pedfile, outfile, phen, covars = NULL)
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 phenfile |
covars |
a character vector for covariates in phenfile |
Similar to the details for 'gee.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 beta |
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 chi-square statistic |
Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>