gwSnpScreenResult-class {GGtools} | R Documentation

## Class "gwSnpScreenResult" – containers for genome-wide and chromosome-wide snp screen statistics

### Description

Class "gwSnpScreenResult" – containers for genome-wide and chromosome-wide snp screen statistics

### Objects from the Class

Objects can be created by calls of the form `new("gwSnpScreenResult", ...)`. Mild extensions to 'list'.

### Slots

`.Data`:
  Object of class `"list"` list of data.frames or matrices of test results
`gene`:
  Object of class `"character"` gene name
`psid`:
  Object of class `"character"` probe identifier
`annotation`:
  Object of class `"character"` – propagated from smlSet
`snpLocExtRef`:
  Object of class `"character"`, full pathname of external store for snp locations relevant to the smlSet instance from which gwSnpScreenResult was computed.

### Extends

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

### Methods

plot
  `signature(x = "gwSnpScreenResult", y = "ANY")`: plots minus log p values of association tests along chromosomal coordinates
show
  `signature(object = "gwSnpScreenResult")`: brief report
[
  `signature(object = "gwSnpScreenResult")`: restricts chromosomes represented

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### Examples

    showClass("gwSnpScreenResult")
    data(hmceuB36.2021)
    objects("package:GGBase")
    x = gwSnpScreen(genesym("CPNE1"), hmceuB36.2021, chrnum(20))
    x

[Package GGtools version 2.0.2 Index]