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GGtools (version 5.8.0)

software and data for analyses in genetics of gene expression

Description

software and data for analyses in genetics of gene expression and/or DNA methylation

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Version

Version

5.8.0

License

Artistic-2.0

Maintainer

Vince Carey

Last Published

February 15th, 2017

Functions in GGtools (5.8.0)

sensiCisOutput-class

Class "sensiCisOutput"
eqtlTests

compute association statistics between all probes and SNP in an smlSet instance
qqhex

obtain qqplot coordinates for the specific case of comparing a given distribution to that of multiple realizations from a permutation distribution, and bin these coordinates using hexbin, useful for very large samples
gwSnpTests

execute a series of tests for association between genotype and expression
snplocsDefault

name the default SNPlocs.Hsapiens.dbSNP.* package
ex

ExpressionSet instance for illustrating integrative smlSet container
eqtlTests.me

use MatrixEQTL computations and statistics as a back end to GGtools eqtlTests
best.trans.eQTLs

collect strongest trans SNP-gene associations in a buffer of size K genes per SNP
sensanal

Summarize information from a collection of eQTL searches for sensitivity assessment
bindmaf

bind testing metadata to a best.cis.eQTLs result
All.cis

functions that compute score tests for all SNP cis to genes, with flexible filtering
gffprocess

transform a collection of gff3 into a single tabix-indexed gff3
transTab

tabulate results of transScores run
EqAppr-class

Class "EqAppr"
getCisMap

create, using Bioconductor annotation resources, a structure that enumerates SNP in the vicinity of ('cis' to) genes
transManager-class

Class "transManager"
richNull

bind metadata concerning SNP allele frequency and other aspects of optimized cis-eQTL association to an mcwBestCis instance
transScores

obtain the top trans associations for each SNP in an smlSet
cisRun-class

Class "cisRun"
TransConfig-class

Class "TransConfig"
sampsInVCF

enumerate samples available in a VCF file
b1

mcwBestCis instances, integrative analysis output containers generated by GGtools vignette
vcf2sm

generate a SnpMatrix instance on the basis of a VCF (4.0) file
CisConfig-class

Class "CisConfig"
eqsens_dt

support for sensitivity analyses related to eQTL enumerations
best.cis.eQTLs

collect genewise best scoring eQTL
appraise

appraisal for eQTL prediction models
simpleTiling

create a GRanges with a tiling of the human genome
GGtools-package

software and data for analyses in genetics of gene expression
collectBest

given a collection of All.cis outputs (cisRun instances) compute FDRs for various filterings
ciseqByCluster

end-to-end cluster-based cis-eQTL search, and allied utilities
strMultPop

serialization of a table from Stranger's multipopulation eQTL report
eqBox

descriptive plot of expression against genotype for cisAssoc results
sensiCisInput-class

Class "sensiCisInput"
hmm878

labeled GRanges with ChromHMM chromatin states for GM12878
concatCis

combine a list of cisRun instances to a single instance
eqtlTestsManager-class

Class "eqtlTestsManager"
scoresCis

visualize a gene model with cis-eQTL association scores (-log FDR by default) on the basis of a ciseqByCluster data.table output
transeqByCluster

convenience functions for trans-eQTL testing
cgff2dt

translate the GFF3 from a ciseqByCluster/processgff output into a serialized data.table instance, compute genome-wide plug-in FDR, and update the GFF3 with this FDR
pifdr

utility for computing plug-in FDR
cisAssoc

test for variant-expression associations in cis, using VCF