GGtools-package |
GGtools Package Overview |
checkCommonSNPs |
confine the SNPs (in multiple chromosomes) in all elements of a list of smlSets to the largest shared subset per chromosome; test for satisfaction of this condition |
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 |
cisProxScores |
create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions |
cisProxScores-class |
Class "cisProxScores" |
cisTransDirector-class |
Class "eqtlTestsManager" |
clipPCs |
simple approach to removal of principal components from smlSet |
degnerASE01 |
transcription of a table from a paper by Degner et al |
eqtlTests |
perform genome x transcriptome eQTL searches with high-performance options |
eqtlTestsManager-class |
Class "eqtlTestsManager" |
ex6 |
example exon region data |
exome_minp |
acquire minimum p-value for association between genotype and expression |
externalize |
create R package with decomposable smlSet representation |
getSS |
create R package with decomposable smlSet representation |
GGtools |
GGtools Package Overview |
gwSnpTests |
methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
gwSnpTests-method |
methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
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 |
imphm3_1KG_20_mA2 |
snpStats-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only |
imphm3_1KG_20_mA5 |
snpStats-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only |
interleave2cis |
create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions |
m20 |
snpStats (1.1.1) with imputed genotypes for 110 HapMap phase III samples from CEU population |
makeCommonSNPs |
confine the SNPs (in multiple chromosomes) in all elements of a list of smlSets to the largest shared subset per chromosome; test for satisfaction of this condition |
makeDiagDirector |
Class "multiCisDirector" |
manhPlot |
manhattan plot for an eqtlTests result |
mcisProxScores |
create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions |
mkCisTransDirector |
Create an object that manages a collection of eqtlTestManagers |
multffCT |
parallelized multipopulation cis-trans eQTL searches |
multiCisDirector-class |
Class "multiCisDirector" |
pcChooser |
utility to assist in choosing number of PCs to remove owing to expression heterogeneity |
permEx |
permute expression data against genotype data in an smlSet |
plot-method |
Methods for Function plot in Package 'GGtools' |
probeNames |
Class "eqtlTestsManager" |
probeNames-method |
Class "eqtlTestsManager" |
relocate |
assist in the transport between systems of ff data managed by GGtools |
residTests |
methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
residTests-method |
methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
show-method |
Class "cisProxScores" |
show-method |
Class "eqtlTestsManager" |
show-method |
Class "multiCisDirector" |
show-method |
generate a SnpMatrix instance on the basis of a VCF (4.0) file |
strMultPop |
serialization of a table from Stranger's multipopulation eQTL report |
topFeats |
compute numerical matrix of chisq statistics in a genomic interval; extract features as requested |
topFeats-method |
compute numerical matrix of chisq statistics in a genomic interval; extract features as requested |
topSnps |
report on most significant SNP with gwSnpTests results |
topSnps-method |
report on most significant SNP with gwSnpTests results |
topSnps-methods |
report on most significant SNP with gwSnpTests results |
vcf2sm |
generate a SnpMatrix instance on the basis of a VCF (4.0) file |
X2chunk |
compute numerical matrix of chisq statistics in a genomic interval; extract features as requested |
[-method |
Class "eqtlTestsManager" |