Man pages for oncogenetics/oncofunco
Custom function for Oncogenetics team
| 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 |
