gwSnpScreenResult-class {GGBase}R Documentation

Class "gwSnpScreenResult" – container 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.

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
snpLocPackage:
Object of class "character" name of package holding the netCDF store of SNP locations
snpLocExtRef:
Object of class "character" name of object in snpLocPackage pointing to the external store (SQLite)
activeSnpInds:
Object of class "numeric" vector telling which SNPs (relative to the referenced netCDF locations store) were used

Extends

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

Methods

No methods defined with class "gwSnpScreenResult" in the signature in class GGBase. See GGtools gwSnpScreen documentation.

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples

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

[Package GGBase version 2.0.4 Index]