GGtools-package {GGtools} | R Documentation

## software and data for analyses in genetics of gene expression

### Description

software and data for analyses in genetics of gene expression

### Details

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.

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

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

### See Also

`getSS` for acquiring containers for integrative data on genetics of expression.

### Examples

    ## 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)

[Package GGtools version 5.16.0 Index]