fitNullReg {GENESIS} | R Documentation |
fitNullReg
fits a regression model. The output of fitNullReg
can be passed to assocTestSeq
or assocTestSeqWindow
for the purpose of genetic association testing.
fitNullReg(scanData, outcome, covars = NULL, scan.include = NULL, family = gaussian, verbose = TRUE)
scanData |
An object of class |
outcome |
A character string specifying the name of the outcome variable in |
covars |
A vector of character strings specifying the names of the fixed effect covariates in |
scan.include |
A vector of scanIDs for samples to include in the analysis. If NULL, all samples in |
family |
A description of the error distribution to be used in the model. The default "gaussian" fits a linear model; see |
verbose |
Logical indicator of whether updates from the function should be printed to the console; the default is TRUE. |
An object of class 'GENESIS.nullModel
'. A list including:
fixef |
A data.frame with effect size estimates (betas), standard errors, chi-squared test statistics, and p-values for each of the fixed effect covariates specified in |
betaCov |
The estimated covariance matrix of the effect size estimates (betas) of the fixed effect covariates. This can be used for hypothesis tests regarding the fixed effects. |
resid.response |
The residuals from the model. |
logLik |
The log-likelihood value. |
AIC |
The Akaike Information Criterion value. |
workingY |
The "working" outcome vector. When |
model.matrix |
The design matrix for the fixed effect covariates used in the model. |
aliased |
Coefficients removed from the model. |
sigma |
Variance of the model. |
scanID |
A vector of scanIDs for the samples used in the analysis. |
family |
A character string specifying the family used in the analysis. |
Matthew P. Conomos