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]