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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

License

Artistic-2.0

Maintainer

Vince Carey

Last Published

February 15th, 2017

Functions in gQTLstats (1.4.2)

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