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 |
cisRanges |
create GRanges instance for intervals cis to a set of genes |
cisScores |
perform genome x transcriptome eQTL searches with high-performance options |
cisSnpTests |
perform tests for eQTL cis to specified genes |
cisTransDirector-class |
Class "eqtlTestsManager" |
coerce-method |
Class "multffManager" |
coerce-method |
Transform results of gwSnpTests to browser tracks |
degnerASE01 |
transcription of a table from a paper by Degner et al |
diagffCC |
perform a 'diagonal' cis eQTL search (only check SNPs chromosomally coresident with genes) |
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 |
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) |
getGRanges |
acquire a GRanges instance with eQTL scores for all SNP for a given gene |
getNamedLocs |
get a named vector of SNP locations |
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 |
ieqtlTests |
perform genome x transcriptome eQTL searches with high-performance options |
imphm3_1KG_20_mA2 |
snpMatrix-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only |
imphm3_1KG_20_mA5 |
snpMatrix-generated rules from imputing from HapMap phase III loci to 1000 genomes loci - for chromosome 20 only |
m20 |
snpMatrix (1.3.13) 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 |
manhPlot |
manhattan plot for an eqtlTests result |
maxchisq |
Class "maxchisq" |
maxchisq-class |
Class "maxchisq" |
meqtlTests |
perform genome x transcriptome eQTL searches with high-performance options |
min_p_vals |
Class "maxchisq" |
min_p_vals-method |
Class "maxchisq" |
mkCisTransDirector |
Create an object that manages a collection of eqtlTestManagers |
multffCT |
parallelized multipopulation cis-trans eQTL searches |
multffManager-class |
Class "multffManager" |
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" |
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 |
scoresInRanges |
structured survey of eqtlTestsManager to retrieve scores cis to genes |
show-method |
Class "eqtlTestsManager" |
show-method |
Class "maxchisq" |
show-method |
Class "multffManager" |
show-method |
generate a snp.matrix instance on the basis of a VCF (4.0) file |
snp130locs |
prototypical function for creation of IRanges-based SNP location data |
snpLocs20 |
prototype SNP location instance for use with GGtools |
snpLocs_21 |
prototype SNP location instance for use with GGtools |
strMultPop |
serialization of a table from Stringer'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 snp.matrix 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" |
[-method |
Class "multffManager" |