Objects | Description |
| eQTL/GWAS |
| |
get.prop.below.LLOD | Limit of detection analysis |
import_eQTLCatalogue | Import eQTL Catalogue |
import_OpenGWAS | Import OpenGWAS |
make_ExpressionSet | A call to ExpressionSet class |
novelty_check | Locus novelty check |
run_coloc | Colocalisation analysis |
| MR analysis |
| |
pqtlMR | Bidirectional pQTL-MR analysis |
qtl_lookup | QTL lookup |
run_TwoSampleMR | A generic wrapper for TwoSampleMR analysis |
| PhenoScanner Utilities |
| |
genequeries | phenoscanner genequeries in batches |
regionqueries | phenoscanner regionqueries in batches |
snpqueries | phenoscanner snpqueries in batches |
| UniProt API |
| |
uniprot2ids | UniProt ID to others |
| Functions in R/gap |
| |
METAL_forestplot | Forest plots from metal analysis |
cis.vs.trans.classification | a cis/trans classifier |
circos.cis.vs.trans.plot | circos plot of cis/trans classification |
circos.mhtplot | circos Manhattan plot with gene annotation |
circos.mhtplot2 | Another circos Manhattan plot |
cs | Credible set |
get_b_se | Get b and se from AF, n, and z |
get_pve_se | Get pve and its standard error from n, z |
get_sdy | Get sd(y) from AF, n, b, se |
gsmr | Mendelian randomization analysis |
invnormal | Inverse normal transformation |
log10p | log10(p) for a standard normal deviate |
log10pvalue | log10(p) for a P value including its scientific format |
logp | log(p) for a normal deviate |
mhtplot.trunc | Truncated Manhattan plot |
miamiplot2 | Miami plot |
mr_forestplot | Mendelian Randomization forest plot |
qtlClassifier | A QTL cis/trans classifier |
qtl2dplot | 2D QTL plot |
qtl2dplotly | 2D QTL plotly |
qtl3dplotly | 3D QTL plotly |