gwSnpScreenResult-class {GGBase} | R Documentation

## Class "gwSnpScreenResult" – containers for GGtools gwSnpScreen method outputs and allied objects

### Description

Class "gwSnpScreenResult" – container for GGtools gwSnpScreen method outputs and allied objects

### Objects from the Class

Objects can be created by calls of the form `new("gwSnpScreenResult", ...)`. These will be primarily lists of inference tables (snps are rows, columns are statistics and p-values). Additional slots manage analysis metadata.

gwSnpScreenResult is intended for genome-wide analysis of expression for a single gene.

cwSnpScreenResult is intended for the restriction to a single chromosome.

multiGwSnpScreenResult is intended for analyses with multiple genes.

Because the vast majority of tests are uninformative, early filtering is important for managing object sizes. Instances of filteredGwSnpScreenResult and filteredMultiGwSnpScreenResult are created when a texttt{snpdepth} parameter is used with gwSnpTests.

### Slots

`.Data`:
  Object of class `"list"` containing inference tables (snps are rows, columns are statistics and p-values)
`gene`:
  Object of class `"character"` typically the HUGO symbol of the gene analyzed
`psid`:
  Object of class `"character"` the feature identifier of the associated microarray
`annotation`:
  Object of class `"character"` vector of relevant annotation package identifier names
were used

`formula`:
  Object of class `"formula"` the formula used to fit the model relating expression to genotype

### Extends

Class `"list"`, from data part. Class `"vector"`, by class "list", distance 2. Class `AssayData`, by class "list", distance 2.

### Methods

plot and show

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### Examples

    showClass("gwSnpScreenResult")
    showClass("cwSnpScreenResult")

[Package GGBase version 3.0.0 Index]