gQTLstats-package {gQTLstats} | R Documentation

## gQTLstats: computationally efficient analysis for eQTL and allied studies

### Description

computationally efficient analysis of eQTL, mQTL, dsQTL, etc.

### Details

The DESCRIPTION file:

Package: | gQTLstats
Title: | gQTLstats: computationally efficient analysis for eQTL and allied studies
Version: | 1.12.0
Author: | VJ Carey <stvjc@channing.harvard.edu>
Description: | computationally efficient analysis of eQTL, mQTL, dsQTL, etc.
Suggests: | geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio, BiocStyle, RUnit, multtest, gwascat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, ldblock
Depends: | R (>= 3.1.0), Homo.sapiens
Imports: | methods, snpStats, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicFiles, GenomicRanges, SummarizedExperiment, VariantAnnotation, Biobase, BatchJobs, gQTLBase, limma, mgcv, dplyr, AnnotationDbi, GenomicFeatures, ggplot2, reshape2, doParallel, foreach, ffbase, BBmisc, beeswarm, HardyWeinberg, graphics, stats, utils, shiny, plotly, erma, ggbeeswarm
Maintainer: | VJ Carey <stvjc@channing.harvard.edu>
License: | Artistic-2.0
LazyLoad: | yes
VignetteBuilder: | knitr
BiocViews: | SNP, GenomeAnnotation, Genetics

Index of help topics:

    FDRsupp-class           Class '"FDRsupp"'
    TransStore              Instance constructor for managing trans gQTL
                            results
    TransStore-class        Class '"TransStore"'
    cisAssoc                test for variant-expression associations in cis
                            or generally, using VCF
    clipPCs                 transformations of expression data in smlSet
                            instances
    directPlot              visualize relationship between empirical and
                            modeled FDR based on analysis of a gQTL store
    enumerateByFDR          filter a ciseStore instance using an FDR
                            threshold
    eqBox2                  visualization of expression or other assay
                            measure against genotypes extracted from VCF
    filtFDR                 illustration of FDRsupp class
    gQTLs                   use SummarizedExperiment to manage a collection
                            of gQTL results of interest
    gQTLstats-package       gQTLstats: computationally efficient analysis
                            for eQTL and allied studies
    hmm878                  labeled GRanges with ChromHMM chromatin states
                            for GM12878
    manhWngr                manhattan plot with named GRanges
    mixedVCFtoSnpMatrix     amalgamate called genotypes and imputed allelic
                            dosages in VCF to SnpMatrix representation
    pifdr                   utility for computing plug-in FDR
    qqStore                 create a binned QQplot for a sharded store
    queryVCF                obtain SnpMatrix from VCF genotypes
    senstab                 create a plottable table for eQTL sensitivity
                            analysis visualization
    setFDRfunc              estimate and store function relating
                            association scores to approximate plug-in FDR
    storeToQuantiles        extract a vector from store results as ff (out
                            of memory reference); support statistical
                            reductions
    tqbrowser               general browsing facility for trans-gQTL
    transAssoc              compute 'trans' SNP-feature associations by
                            wrapping AllAssoc
    transBrowse             shiny app to exhibit genotype:genomic feature
                            distributions
    tsByRank                harvest contents of a TransStore by rank in
                            associations of features to SNP
    txsPlot                 visualize transformed FDR against transformed
                            association statistics

This package addresses the management of map-reduce like computations for cis-association tests between DNA variants and genomic features like gene expression measurements. It makes essential use of data structures defined in package gQTLBase.

A number of experimental functions are present in the current version of the package: prep.cisAssocNB (assembles information to assess negative binomial regression in cis association testing), storeToMaxAssocBySNP (progress towards SNP-specific FDR), table_sensobj_thresh (reporting on sensitivity analysis).

Additional experimental functions are available to support scalable trans-gQTL testing TransChunk, filteredDFwPerm, and transTable operate on output of AllAssoc.

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Maintainer: VJ Carey <stvjc@channing.harvard.edu>

[Package gQTLstats version 1.12.0 Index]