lme.batch.imputed {GWAF} | R Documentation |
Fit linear mixed effects model to test association between a continuous phenotype
and all imputed SNPs in a genotype file. The SNP genotype is treated
as fixed effects, and a random effect correlated according to degree of relatedness within a
family is also fitted. In each trait-SNP assocaition test, the lmekin()
function which is modified from
the same named function in package kinship
is used.
lme.batch.imputed(phenfile, genfile, pedfile, phen, kinmat, covars=NULL, outfile, col.names=T, sep.ped=",", sep.phe=",", sep.gen=",")
phenfile |
a character string naming the phenotype file for reading (see format requirement in details) |
genfile |
a character string naming the genotype file for reading (see format requirement in details) |
pedfile |
a character string naming the pedigree file for reading (see format requirement in details) |
phen |
a character string for a phenotype name in phenfile |
kinmat |
a character string naming the file where kinship coefficient matrix is kept |
covars |
a character vector for covariates in phenfile |
outfile |
a character string naming the result file for writing |
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 lme.batch
function 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 |
AF |
imputed allele frequency of coded allele |
h2q |
the portion of phenotypic variation explained by the SNP |
beta |
regression coefficient of SNP covariate |
se |
standard error of beta |
pval |
p-value of the chi-square statistic |
Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>
kinship package: mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees. Beth Atkinson (atkinson@mayo.edu) for pedigree functions.Terry Therneau (therneau@mayo.edu) for all other functions. 2007. Ref Type: Computer Program http://cran.r-project.org/.
Abecasis, G. R., Cardon, L. R., Cookson, W. O., Sham, P. C., & Cherny, S. S. Association analysis in a variance components framework. Genet Epidemiol, 21 Suppl 1, S341-S346 (2001).