CisConfig-class: Class '"CisConfig"'

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

Description

Object specifying configuration of cis-eQTL search, to be used with All.cis

Objects from the Class

Objects can be created by calls of the form new("CisConfig"). Use replacement methods to update the fields.

Slots

smpack:

character string identifying package holding the expression and genotype data; see getSS

genome:

character string identifying genome build in use

rhs:

Object of class "formula" right hand side for calls to snp.rhs.tests

nperm:

Object of class "integer" number of permutations for plug in FDR

folderStem:

Object of class "character" string used for scratch space folders, relative to current folder

radius:

Object of class "integer" radius of search

shortfac:

Object of class "integer" scores are scaled up by this factor so that precision can be retained in short integer representation

chrnames:

Object of class "character" string identifying chromosome label used in gene annotation retrieval – typically length 1

smchrpref:

Object of class "character" prefix to be attached to chromosome label in chrnames to pick out the element of smlSet-class instance used in testing

gchrpref:

Object of class "character" prefix on chrnames token to be used for gene location retrievals

schrpref:

Object of class "character" prefix on chrnames token to be used with SNPlocs package for retrieval of SNP locations

geneApply:

Object of class "function" iterator over genes, could be lapply or mclapply

geneannopk:

Object of class "character" Bioconductor annotation package for gene locations, typically for expression array

snpannopk:

Object of class "character" Bioconductor dbSNP annotation package

smFilter:

Object of class "function" function to be applied to smlSet instance that yields an smlSet instance with required contents; could apply MAF restriction for example by calling MAFfilter

exFilter:

Object of class "function" function that is run right after smlSet is materialized, permitting replacement or filtering of expression data, when, for example, the ExpressionSet includes multiple tissue types

keepMapCache:

Object of class "logical" for enhancing processing of gene-SNP cis mapping with a global cache

SSgen:

Object of class "function" function that accepts name of an expression+SnpMatrix package (as generated by externalize), a chromosome tag (chrnames prefixed by smchrpref), and a function, and returns an smlSet instance

excludeRadius:

Object of class "integerOrNULL" which will determine what interval about the gene is excluded for cis testing; 0 should exclude all within-gene SNP, but needs testing

estimates:

Object of class "logical" if TRUE, estimates and standard errors (expanded and reduced in storage as a short int, using shortfac) are generated and retained

extraProps:

Object of class "function" this function is applied to the cisScores output before it is returned, to bind additional metadata to the ranges if desired. Defaults to function(x)x.

useME:

Object of class "logical" if TRUE, use the statistics generated by Matrix_eQTL_engine for association testing.

MEpvot:

Object of class "numeric" used if useME slot is set to TRUE: p-value output threshold for retaining association test statistic generated by Matrix_eQTL_engine; defaults to 0.5. Higher values lead to higher volumes and longer times to completion.

Methods

chrnames

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

chrnames<-

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

estimates

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

estimates<-

signature(object = "CisConfig", value = "logical"): ...

excludeRadius

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

excludeRadius<-

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

exFilter

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

exFilter<-

signature(object = "CisConfig", value = "function"): ...

gchrpref

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

gchrpref<-

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

geneannopk

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

geneannopk<-

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

geneApply

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

geneApply<-

signature(object = "CisConfig", value = "function"): ...

initialize

signature(.Object = "CisConfig"): ...

keepMapCache

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

keepMapCache<-

signature(object = "CisConfig", value = "logical"): ...

radius

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

radius<-

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

rhs

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

rhs<-

signature(object = "CisConfig", value = "function"): ...

schrpref

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

schrpref<-

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

shortfac

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

shortfac<-

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

show

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

smchrpref

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

smchrpref<-

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

smFilter

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

smFilter<-

signature(object = "CisConfig", value = "function"): ...

snpannopk

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

snpannopk<-

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

SSgen

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

SSgen<-

signature(object = "CisConfig", value = "function"): ...

Examples

showClass("CisConfig")

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