GGtools (version 5.8.0)

GGtools-package: 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.

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)