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ObjectsDescription
eQTL/GWAS
get.prop.below.LLODLimit of detection analysis
import_eQTLCatalogueImport eQTL Catalogue
import_OpenGWASImport OpenGWAS
make_ExpressionSetA call to ExpressionSet class
novelty_checkLocus novelty check
run_colocColocalisation analysis
MR analysis
pqtlMRBidirectional pQTL-MR analysis
qtl_lookupQTL lookup
run_TwoSampleMRA generic wrapper for TwoSampleMR analysis
PhenoScanner Utilities
genequeriesphenoscanner genequeries in batches
regionqueriesphenoscanner regionqueries in batches
snpqueriesphenoscanner snpqueries in batches
UniProt API
uniprot2idsUniProt ID to others
Functions in R/gap
METAL_forestplotForest plots from metal analysis
cis.vs.trans.classificationa cis/trans classifier
circos.cis.vs.trans.plotcircos plot of cis/trans classification
circos.mhtplotcircos Manhattan plot with gene annotation
circos.mhtplot2Another circos Manhattan plot
csCredible set
get_b_seGet b and se from AF, n, and z
get_pve_seGet pve and its standard error from n, z
get_sdyGet sd(y) from AF, n, b, se
gsmrMendelian randomization analysis
invnormalInverse normal transformation
log10plog10(p) for a standard normal deviate
log10pvaluelog10(p) for a P value including its scientific format
logplog(p) for a normal deviate
mhtplot.truncTruncated Manhattan plot
miamiplot2Miami plot
mr_forestplotMendelian Randomization forest plot
qtlClassifierA QTL cis/trans classifier
qtl2dplot2D QTL plot
qtl2dplotly2D QTL plotly
qtl3dplotly3D QTL plotly

Author

Jing Hua Zhao in collaboration with other colleagues