sensiCisInput-class {GGtools} | R Documentation

## Class `"sensiCisInput"`

### Description

Manage references to collections of cis-eQTL searches for sensitivity analysis.

### Objects from the Class

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

### Slots

`cisMgrFiles`:

  Object of class `"character"`: a vector of filenames, each file is an instance of class `mcwBestCis-class`

`cisMgrProperties`:

  Object of class `"list"` one vector with named elements per element of `cisMgrFiles`, with components `rad`, `excl`, `maf`, `nperm`, `npc`; see details below.

`probeannopk`:

  Object of class `"character"`, identifying a bioconductor probe annotation package that can be used to map probe identifiers to other vocabularies or feature value sets

### Methods

sensanal

  `signature(object = "sensiCisInput", fdrbound = "numeric")`: generates an instance of `sensiCisOutput-class` with summarization of sensitivities

show

  `signature(object = "sensiCisInput")`: concise rendering

### Note

This version of sensitivity analysis support is rudimentary and involves manual construction of metadata that should be extractable from analysis outputs. The radius of the cis search (and radius of excluded interior if used) are identified as elements named `rad` and `excl` in the `cisMgrProperties` vectors; additional elements `maf`, `nperm`, and `npc` define the lower bound for minor allele frequency, number of permutations for plug-in FDR computation, and number of principal components removed to adjust for expression heterogeneity in the associated cis-eQTL search.

### Examples

    showClass("sensiCisInput")

[Package GGtools version 5.22.0 Index]