getSummary {CGEN} | R Documentation

## Compute summary information

### Description

Returns a matrix of estimated parameters, standard errors, test statistics, and p-values.

### Usage

     getSummary(fit, sided=2, method=NULL)

### Arguments

`fit` | The return object from `snp.logistic`, `snp.matched`, `glm()`, or a list with names "parms" and "cov" containing parameter estimates and the variance-covariance matrix for the estimates. No default.
`sided` | 1 or 2 for a 1 or 2 sided p-values. The default is 2.
`method` | Vector of values from "UML", "CML", "EB" or "CCL", "HCL", "CLR". The default is NULL.

### Details

This function returns a matrix similar to `summary(glm.obj)$coefficients`, except the p-values are always computed using the normal distribution.

### Value

A matrix with column names "Estimate", "Std.Error", "Z.value", and "Pvalue". The rownames of the returned matrix will be the names of `parms` if `parms` is a vector.

### Examples

     parms <- 1:5
     cov   <- matrix(data=1, nrow=5, ncol=5)
     getSummary(list(parms=parms, cov=cov))

     # Compare to summary()
     # set.seed(123)
     n <- 100
     y <- rbinom(n, 1, 0.5)
     x <- cbind(runif(n), rbinom(n, 1, 0.5))
     fit <- glm(y ~ x, family=binomial())
     sum <- summary(fit)
     sum$coefficients
     getSummary(fit)

[Package CGEN version 3.28.0 Index]