GGtools-package {GGtools} | R Documentation |
software and data for analyses in genetics of gene expression
Package: | GGtools |
Version: | 4.2.26 |
Suggests: | GGdata, illuminaHumanv1.db |
Depends: | R (>= 2.14), GGBase (>= 3.16.1) |
Imports: | methods, snpStats, ff, IRanges, GenomicRanges, AnnotationDbi, Biobase, Rsamtools, bit, VariantAnnotation |
License: | Artistic-2.0 |
LazyLoad: | yes |
Packaged: | 2012-01-18 03:39:51 UTC; stvjc |
Collate: | AllClasses.R AllGenerics.R eqtlTests.R managers.R topFeats.R gwSnpTests.R snpsCisToGenes.R relocate.R topSnps.R transutils.R vcfutils.R eqtlEstimates.R alleq.R meta.R |
Built: | R 2.15.0; ; 2012-02-06 17:22:52 UTC; unix |
Index:
best.cis.eQTLs collect genewise best scoring eQTL eqtlTests compute association statistics between all probes and SNP in an smlSet instance eqtlTestsManager-class Class '"eqtlTestsManager"' ex ExpressionSet instance for illustrating integrative smlSet container getCisMap create, using Bioconductor annotation resources, a structure that enumerates SNP in the vicinity of ('cis' to) genes gwSnpTests execute a series of tests for association between genotype and expression strMultPop serialization of a table from Stranger's multipopulation eQTL report hg19.si.df data frame representation of seqinfo for Homo.sapiens at hg19 build
The package depends on GGBase, which includes additional infrastructure for integrative data structures and data filtering.
VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
getSS
for acquiring containers for
integrative data on genetics of expression.
## Not run: # acquire chromosome 20 genotypes and all expression data for # 90 CEU samples as published at Wellcome Trust GENEVAR and # HapMap phase II c20 = getSS("GGtools", "20") # perform a focused eQTL search t1 = gwSnpTests(genesym("CPNE1")~male, c20) # get best hits topSnps(t1) ## End(Not run)