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

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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.preprocess

signature(object = "AVS"): see avs.preprocess

avs.vse

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

avs.evse

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

avs.get

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

Author(s)

Mauro Castro

See Also

TNA-class.

Examples

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## Not run: 
#This example requires the RTNdata package! (currently available under request)
library(RTNdata.LDHapMap.rel27)
data(bcarisk) #mapped to the same genome build of the RTNdata!
avs <- new("AVS", markers=bcarisk)

## End(Not run)

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