software and data for genetical genomics (c) 2006 VJ Carey


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Documentation for package ‘GGtools’ version 3.4.0

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GGtools-package GGtools Package Overview
aafSNP Class "aafSNP" - container for HTML rendering of SNP metadata
aafSNP-class Class "aafSNP" - container for HTML rendering of SNP metadata
chunksize methods for iterating association tests (expression vs SNP) across genomes or chromosomes
chunksize-class methods for iterating association tests (expression vs SNP) across genomes or chromosomes
cisSnpTests perform tests for eQTL cis to specified genes
coerce,cwSnpScreenResult,RangedData-method Transform results of gwSnpTests to browser tracks
GGtools GGtools Package Overview
gwSnpTests methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests,formula,smlSet,cnumOrMissing,ANY-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests,formula,smlSet,cnumOrMissing,missing-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests,formula,smlSet,cnumOrMissing-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests,formula,smlSet,snpdepth,ANY-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests,formula,smlSet,snpdepth,chunksize-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests,formula,smlSet,snpdepth,missing-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests,formula,smlSet,snpdepth-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
hbTestResults-class Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
hbTests haplotype-block based tests for structured expression variation
hbTests,genesym,smlSet,chrnum,numeric,numeric-method haplotype-block based tests for structured expression variation
hbTests-methods haplotype-block based tests for structured expression variation
hla2set a gene set of 9 genes from human HLA2 locus
hmceuB36.2021 two chromosomes of genotype data and full expression data for CEPH CEU hapmap data
hscores Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
hscores,hbTestResults-method Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
invokePhase ~~ Methods for Function invokePhase in Package 'GGtools' ~~
invokePhase,phaseInput,chrnum,character,character,character,logical-method ~~ Methods for Function invokePhase in Package 'GGtools' ~~
invokePhase,snp.matrix,chrnum,character,character,character,logical-method ~~ Methods for Function invokePhase in Package 'GGtools' ~~
invokePhase-methods ~~ Methods for Function invokePhase in Package 'GGtools' ~~
locs Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
locs,hbTestResults-method Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
make_smlSet create an smlSet instance from components
masterSnps visualize a multiGwSnpScreenResult
parsePh.out convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE
personalHap convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE
phaseInput-class convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE
plot,cwSnpScreenResult,missing-method Methods for Function plot in Package 'GGtools'
plot,filteredGwSnpScreenResult,ANY-method Methods for Function plot in Package 'GGtools'
plot,filteredMultiGwSnpScreenResult,ANY-method Methods for Function plot in Package 'GGtools'
plot,snp.reg.imputation,missing-method Methods for Function plot in Package 'GGtools'
pvals Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
pvals,hbTestResults-method Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
residTests methods for iterating association tests (expression vs SNP) across genomes or chromosomes
residTests,cwSnpScreenResult,smlSet,formula,missing-method methods for iterating association tests (expression vs SNP) across genomes or chromosomes
smtest prepare input to mapLD function for haplotype block identification
snpm2mapLD prepare input to mapLD function for haplotype block identification
snpm2phase convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE
strMultPop serialization of a table from Stringer's multipopulation eQTL report
topSnps report on most significant SNP with gwSnpTests results
topSnps,cwSnpScreenResult-method report on most significant SNP with gwSnpTests results
topSnps,gwSnpScreenResult-method report on most significant SNP with gwSnpTests results
topSnps-methods report on most significant SNP with gwSnpTests results