allMatch | Match all elements in vector. |
cleanPackages | Remove all non-default packages from session. |
colourHue | ggplot2 colours |
extractRsid | Extract rsid |
frr | Calculate Familial Relative Risk (FRR) |
gen2dose | Convert IMPUTE2 gen to dose |
gen2vcf | Convert IMPUTE2 gen to VCFv4.1 format, input for fastqtl |
geneSymbol | Get genes as GRanges object |
getMAF | Calculate MAF |
glmSummary | A formatted output for glm() object |
hyperlink | LocusExplorer hyperlinks for SNPs and geneSymbols |
ICRcolours | ICR colours |
plotAnnot | LocusExplorer - Annotation plot, collapsed |
plotBlank | Blank plot |
plotEQTL | LocusExplorer - TCGA eQTL plot |
plotGene | Plot genes using ggbio::geom_alignment |
plotHistone | LocusExplorer - ENCODE histone track plot |
plotLD | LocusExplorer - LD plot |
plotLDarc | LocusExplorer - LDarc plot |
plotLDmatrix | LocusExplorer - LD plot matrix heatmap |
plotManhattan | LocusExplorer - Manhattan plot |
plotMiami | Miami plot |
plotSNPtype | LocusExplorer - SNP type plot |
shadeTintColour | Shade and tints for input colour |
strPadLeft | Left pad strings. |
theme_LE | LocusExplorer ggplot custom theme |
uniqueBimVariant | Fix Plink BIM file variant IDs when missing or duplicated |
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