CisConfig-class {GGtools} | R Documentation

## Class `"CisConfig"`

### 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")

[Package GGtools version 5.16.0 Index]