AVS-class {RTN} | R Documentation

## Class `"AVS"`: an S4 class for variant set enrichment analysis.

### Description

This S4 class includes a series of methods to do enrichment analyses in Associated Variant Sets (AVSs).

### Objects from the Class

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

### Slots

`markers`:

  Object of class `"character"`, a data frame, a 'BED file' format with rs# markers mapped to the same genome build of the LD source in the RTNdata package.

`validatedMarkers`:

  Object of class `"data.frame"`, a data frame with genome positions of the validated markers.

`variantSet`:

  Object of class `"list"`, an associated variant set.

`randomSet`:

  Object of class `"list"`, a random associated variant set.

`para`:

  Object of class `"list"`, a list of parameters for variant set enrichment analysis.

`results`:

  Object of class `"list"`, a list of results (see return values in the AVS methods).

`summary`:

  Object of class `"list"`, a list of summary information for `markers`, `para`, and `results`.

`status`:

  Object of class `"character"`, a character value specifying the status of the AVS object based on the available methods.

### Methods

avs.vse

  `signature(object = "AVS")`: see `avs.vse`

avs.evse

  `signature(object = "AVS")`: see `avs.evse`

avs.rvse

  `signature(object = "AVS")`: see `avs.rvse`

avs.pevse

  `signature(object = "AVS")`: see `avs.pevse`

avs.get

  `signature(object = "AVS")`: see `avs.get`

### Author(s)

Mauro Castro

### See Also

`TNA-class`

### Examples

    ## Not run:
    #This example requires the RTNdata package! (currently available under request)
    library(RTNdata.LDHapMapRel27.hg18)
    data(bcarisk, package = "RTNdata.LDHapMapRel27.hg18")
    avs <- avs.preprocess.LDHapMapRel27.hg18(bcarisk, nrand=100)

    ## End(Not run)

[Package RTN version 2.16.0 Index]