AVS-class {RTN} | R Documentation |
"AVS"
: an S4 class for variant set enrichment analysis.This S4 class includes a series of methods to do enrichment analyses in Associated Variant Sets (AVSs).
Objects can be created by calls of the form new("AVS", markers)
.
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.
signature(object = "AVS")
: see avs.vse
signature(object = "AVS")
: see avs.evse
signature(object = "AVS")
: see avs.pevse
signature(object = "AVS")
: see avs.get
Mauro Castro
TNA-class
avs.preprocess.LDHapMapRel27
## Not run: #This example requires the RTNdata package! (currently available under request) library(RTNdata.LDHapMapRel27) data(bcarisk) #mapped to the same genome build of the RTNdata! avs <- new("AVS", markers=bcarisk) # see the 'avs.preprocess.LDHapMapRel27' constructor ## End(Not run)