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gQTLstats (version 1.4.2)
gQTLstats: computationally efficient analysis for eQTL and allied studies
Description
computationally efficient analysis of eQTL, mQTL, dsQTL, etc.
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Version
Version
1.4.2
1.4.1
1.2.0
1.0.0
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Version
1.4.2
License
Artistic-2.0
Maintainer
Vince Carey
Last Published
January 1st, 1970
Functions in gQTLstats (1.4.2)
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mixedVCFtoSnpMatrix
amalgamate called genotypes and imputed allelic dosages in VCF to SnpMatrix representation
txsPlot
visualize transformed FDR against transformed association statistics
clipPCs
transformations of expression data in smlSet instances
manhWngr
manhattan plot with named GRanges
TransStore-class
Class
"TransStore"
qqStore
create a binned QQplot for a sharded store
directPlot
visualize relationship between empirical and modeled FDR based on analysis of a gQTL store
senstab
create a plottable table for eQTL sensitivity analysis visualization
hmm878
labeled GRanges with ChromHMM chromatin states for GM12878
filtFDR
illustration of FDRsupp class
TransStore
Instance constructor for managing trans gQTL results
gQTLstats-package
gQTLstats
transAssoc
compute 'trans' SNP-feature associations by wrapping AllAssoc
eqBox2
visualization of expression or other assay measure against genotypes extracted from VCF
queryVCF
obtain SnpMatrix from VCF genotypes
enumerateByFDR
filter a ciseStore instance using an FDR threshold
FDRsupp-class
Class
"FDRsupp"
setFDRfunc
estimate and store function relating association scores to approximate plug-in FDR
pifdr
utility for computing plug-in FDR
gQTLs
use SummarizedExperiment to manage a collection of gQTL results of interest
storeToStats
extract a vector from store results as ff (out of memory reference); support statistical reductions
cisAssoc
test for variant-expression associations in cis, using VCF