gQTLbrowse: interactive exploration of eQTL results
In vjcitn/gQTLbrowser: interactive exploration of gQTL results

Description Usage Arguments Details Value Examples

interactive exploration of eQTL results; code as of jan 6 2015 is written with selectizeInput to throw an error on gene symbol deletion

1 2	gQTLbrowse(store, baseSE, stateGR, phenGR, FDRsupp, orgDbObj = Homo.sapiens, selector=selectizeInput)

`store`	instance of `ciseStore-class`
`baseSE`	a `SummarizedExperiment-class` instance that will be used to get gene-level metadata; the rowData component should include fields `gene\_name`, `gene\_type`
`stateGR`	a `GRanges-class` instance with metadata field `name` that is used to define ‘state’ of range; used with chromHmm labeling by default
`phenGR`	a GRanges instance with disease association labeling in a metadata field `Disease.Trait`; currently the examples depend on the GEUVADIS data and the GEUVADIS SNP identifiers are assumed given in metadata field `geuvvid`
`FDRsupp`	an instance of `FDRsupp-class` that provides a function mapping from association scores to FDR estimates
`orgDbObj`	an AnnotationDbi OrgDb instance such as `Homo.sapiens` to be used for transcript location

currently coded to simplify exposure of an error when selectizeInput is used

side effects: will open browser window and allow interactive gene selection and hover-over tool tip for locus- or trait-specific metadata reporting

data(ggr19)
library(GenomeInfoDb)
seqlevelsStyle(ggr19) = "NCBI"
library(geuvPack)
data(geuFPKM)
library(gQTLBase)
library(geuvStore2)
prst = makeGeuvStore2()
data(ggr19)
data(filtFDR)
library(gQTLstats)
data(hmm878)
seqlevelsStyle(hmm878) = "NCBI"
library(Homo.sapiens)
#
# will throw error when gene symbol in input box is deleted
# but will simply select properly if it is not; change selector to
# selectInput for simpler interface
#
print( gQTLbrowse( prst, geuFPKM, stateGR = hmm878, 
     phenGR = ggr19, FDRsupp = filtFDR, selector=selectInput ) )