| gQTLBase-package {gQTLBase} | R Documentation |
Infrastructure for eQTL, mQTL and similar studies.
The DESCRIPTION file:
| Package: | gQTLBase |
| Title: | gQTLBase: infrastructure for eQTL, mQTL and similar studies |
| Version: | 1.19.0 |
| Author: | VJ Carey <stvjc@channing.harvard.edu> |
| Description: | Infrastructure for eQTL, mQTL and similar studies. |
| Suggests: | geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, GGtools, Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack |
| Imports: | GenomicRanges, methods, BatchJobs, BBmisc, S4Vectors, BiocGenerics, foreach, doParallel, bit, ff, rtracklayer, ffbase, GenomicFiles, SummarizedExperiment |
| Depends: | |
| Maintainer: | VJ Carey <stvjc@channing.harvard.edu> |
| License: | Artistic-2.0 |
| LazyLoad: | yes |
| VignetteBuilder: | knitr |
| BiocViews: | SNP, GenomeAnnotation, Genetics, DataImport, FunctionalGenomics |
| Collate: | storeS4.R cb2range.R ffapp2.R gtpath.R storeFuncs.R mergeToLoci.R ufeatByTiling.R d.R |
| git_url: | https://git.bioconductor.org/packages/gQTLBase |
| git_branch: | master |
| git_last_commit: | ef8f1f4 |
| git_last_commit_date: | 2019-10-29 |
| Date/Publication: | 2019-11-10 |
Index of help topics:
ciseStore-class Class '"ciseStore"'
describeStore collect basic descriptive statistics on
ciseStore instances
extractByProbes retrieve eqtlTest results from a ciseStore
instance
gQTLBase-package gQTLBase: infrastructure for eQTL, mQTL and
similar studies
mergeCIstates merge ChromImpute chromatin states, or GWAS hit
indicators, to a GRanges
storeApply apply a function over job results in a
ciseStore instance
storeMapResults use batchMapResults infrastructure to process
results in a ciseStore instance
storeToFf extract a vector from store results as ff (out
of memory reference); support statistical
reductions
ufeatByTiling split featurenames of SummarizedExperiment
according to tiling, or to achieve simple
balance within seqnames
Purpose is to define infrastructure on a comprehensive archive of eQTL, mQTL, dsQTL, etc., association statistics.
Package will complement gQTLStats. geuvStore2 is a basic illustration relative to GEUVADIS paper.
matprint is exported from package ff.
VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>