gQTLstats-package {gQTLstats} | R Documentation |
computationally efficient analysis of eQTL, mQTL, dsQTL, etc.
The DESCRIPTION file:
Package: | gQTLstats |
Title: | gQTLstats: computationally efficient analysis for eQTL and allied studies |
Version: | 1.18.0 |
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 (>= 3.5.0), 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 |
git_url: | https://git.bioconductor.org/packages/gQTLstats |
git_branch: | RELEASE_3_10 |
git_last_commit: | fe72a50 |
git_last_commit_date: | 2019-10-29 |
Date/Publication: | 2019-10-29 |
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.
VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>