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 |