TransConfig-class: Class '"TransConfig"'

In GGtools: software and data for analyses in genetics of gene expression

Description

Instances from this class can be input to the transScores function to control a trans-eQTL search.

Objects from the Class

Instances from this class can be input to the transScores function to control a trans-eQTL search. Objects can be created by calls of the form new("TransConfig").

Slots

snpchr:

Object of class "character" identifies the name of the chromosome harboring SNP that will all be used (subject to filtering by smFilter function) in transcriptome-wide searches for associated transcripts

gbufsize:

Object of class "integer", scores for the top gbufsize genes are retained as the search proceeds

batchsize:

Object of class "integer" used in processing ff-based archives for association scores

smpack:

Object of class "character", tells the name of the installed package used for retrieval of expression-genotype data using getSS

rhs:

Object of class "formula", formula used in snp.rhs.tests; typically not used. If plug-in FDR is desired, adjustments should be executed in a regressOut call .

folderStem:

Object of class "character", name of a folder where interim results are sequestered.

radius:

Object of class "integer", defines region around SNP within which genes are considered 'cis' so tests are not conducted.

shortfac:

Object of class "integer" see documentation for CisConfig-class

chrnames:

Object of class "character" see documentation for CisConfig-class

smchrpref:

Object of class "character" see documentation for CisConfig-class

gchrpref:

Object of class "character" see documentation for CisConfig-class

schrpref:

Object of class "character" see documentation for CisConfig-class

geneApply:

Object of class "function" see documentation for CisConfig-class

geneannopk:

Object of class "character" see documentation for CisConfig-class

snpannopk:

Object of class "character" see documentation for CisConfig-class

smFilter:

Object of class "function" see documentation for CisConfig-class

exFilter:

Object of class "function" see documentation for CisConfig-class

keepMapCache:

Object of class "logical" see documentation for CisConfig-class

SSgen:

Object of class "function" see documentation for CisConfig-class

excludeRadius:

Object of class "integerOrNULL" see documentation for CisConfig-class

estimates:

Object of class "logical" see documentation for CisConfig-class

Extends

Class "CisConfig", directly.

Methods

batchsize

signature(x = "TransConfig"): ...

batchsize<-

signature(object = "TransConfig", value = "integer"): ...

gbufsize

signature(x = "TransConfig"): ...

gbufsize<-

signature(object = "TransConfig", value = "integer"): ...

show

signature(object = "TransConfig"): ...

snpchr

signature(x = "TransConfig"): ...

snpchr<-

signature(object = "TransConfig", value = "character"): ...

Examples

showClass("TransConfig")

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.