| 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: | 1.20.0 |
| 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_11 |
| git_last_commit: | 76f19c8 |
| git_last_commit_date: | 2020-04-27 |
| Date/Publication: | 2020-04-27 |
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>