GGtools-package |
GGtools Package Overview |
bestCis |
extract best (or all) cis-associated eQTL from a multffmgr instance |
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 |
cisSnpTests |
perform tests for eQTL cis to specified genes |
coerce-method |
Transform results of gwSnpTests to browser tracks |
diagffCC |
perform a 'diagonal' cis eQTL search (only check SNPs chromosomally coresident with genes) |
geneRanges |
construct a RangedData instance for genes enumerated according to an
annotation .db package |
geneTrack |
create a RangedData structure with multffCT test results (as -log10 p values by default) |
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 |
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 |
maxchisq |
Class "maxchisq" |
maxchisq-class |
Class "maxchisq" |
min_p_vals |
Class "maxchisq" |
min_p_vals-method |
Class "maxchisq" |
multffCT |
parallelized multipopulation cis-trans eQTL searches |
multffManager-class |
Class "multffManager" |
plot-method |
Methods for Function plot in Package '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 "maxchisq" |
show-method |
Class "multffManager" |
snp130locs |
prototypical function for creation of IRanges-based SNP location data |
snpLocs20 |
prototype SNP location instance for use with GGtools |
strMultPop |
serialization of a table from Stringer's multipopulation eQTL report |
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 |
[-method |
Class "multffManager" |