TransConfig-class {GGtools} | R Documentation

## Class `"TransConfig"`

### 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")

[Package GGtools version 5.16.0 Index]