summary,ZlmFit-method {MAST} | R Documentation

## Summarize model features from a `ZlmFit` object

### Description

Returns a `data.table` with a special print method that shows the top 2 most significant genes by contrast. This `data.table` contains columns:

primerid

  the gene

component

  C=continuous, D=discrete, logFC=log fold change, S=combined using Stouffer's method, H=combined using hurdle method

contrast

  the coefficient/contrast of interest

ci.hi

  upper bound of confidence interval

ci.lo

  lower bound of confidence interval

coef

  point estimate

z

  z score (coefficient divided by standard error of coefficient)

Pr(>Chisq)

  likelihood ratio test p-value (only if `doLRT=TRUE`)

Some of these columns will contain NAs if they are not applicable for a particular component or contrast.

### Usage

    ## S4 method for signature 'ZlmFit'
    summary(object, logFC = TRUE, doLRT = FALSE,
      level = 0.95, ...)

### Arguments

`object` | A `ZlmFit` object
`logFC` | If TRUE, calculate log-fold changes, or output from a call to `getLogFC`.
`doLRT` | if TRUE, calculate lrTests on each coefficient, or a character vector of such coefficients to consider.
`level` | what level of confidence coefficient to return. Defaults to 95 percent.
`...` | ignored

### Value

`data.table`

### See Also

print.summaryZlmFit

### Examples

    data(vbetaFA)
    z <- zlm(~Stim.Condition, vbetaFA[1:5,])
    zs <- summary(z)
    names(zs)
    print(zs)
    ##Select `datatable` copmonent to get normal print method
    zs$datatable

[Package MAST version 1.4.1 Index]