eqtlTestsManager-class {GGtools} | R Documentation

## Class `"eqtlTestsManager"`

### Description

manage out-of-memory elements of an eQTL search

### Objects from the Class

Objects can be created by calls of the form `new("eqtlTestsManager", ...)`.

### Slots

`fffile`:

  Object of class `"ff_matrix"` chisquared statistics stored as short ints in ff out of memory file

`call`:

  Object of class `"call"` audit of creation call

`sess`:

  Object of class `"ANY"` session info structure at time of creation

`exdate`:

  Object of class `"ANY"` date at time of creation

`shortfac`:

  Object of class `"numeric"` number by which chisq stats are multiplied to allow recovery of precision

`geneanno`:

  Object of class `"character"` string naming annotation package relevant for probe identifier translation

`df`:

  Object of class `"numeric"` degrees of freedom of chisq stats

`summaryList`:

  Object of class `"list"` list of genotype statistical summaries

### Methods

[

  `signature(x = "eqtlTestsManager", i = "ANY", j = "ANY", drop = "ANY")`: extract chisq statistics properly rescaled from short int to double

show

  `signature(object = "eqtlTestsManager")`: concise report

topFeats

  `signature(feat = "probeId", mgr = "eqtlTestsManager")`: extract highest scores for SNP associated with given probeId

topFeats

  `signature(feat = "rsid", mgr = "eqtlTestsManager")`: extract highest scores for probes associated with given SNP

### Note

instances are created by `eqtlTests`

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### Examples

    showClass("eqtlTestsManager")

[Package GGtools version 5.23.2 Index]