gQTLstats (version 1.4.2)

enumerateByFDR: filter a ciseStore instance using an FDR threshold

Description

filter a ciseStore instance using an FDR threshold

Usage

enumerateByFDR(store, fdrsupp, threshold = 0.05, filter=force,
   ids=NULL, trimToUnit=TRUE)

Arguments

store

instance of ciseStore-class

fdrsupp

instance of FDRsupp-class

threshold

upper bound on FDR to be included

filter

The FDR can be computed for any association score. To return only records satisfying a given filter, supply the filter function here. It may be desirable to carry a filter function from the storeToFDR stage, and this may be considered in future versions.

ids

if NULL, process all results in store, otherwise limit attention to jobs with id values in ids

trimToUnit

plug-in FDR estimates can sometimes lie outside [0,1] owing to sparsity or defects of extrapolation; if this parameter is TRUE, estimated FDR values outside [0,1] are moved to the nearest boundary

Value

• A GRanges instance with store contents to which estFDR is appended for each range. The estFDR quantity is predicted using the GAM model held in the FDRsupp instance.

Details

uses storeApply, which will use BiocParallel infrastructure when available

Examples

require(geuvStore2)
require(gQTLBase)
st = makeGeuvStore2()
data(filtFDR)
filtEnum = enumerateByFDR( st, filtFDR,
  filter=function(x)x[which(x$mindist <= 500000 & x$MAF >= 0.05)] )
names(metadata(filtEnum))
filtEnum[order(filtEnum$chisq, decreasing=TRUE)[1:2]]