| acc | Compute prediction accuracy for a quantitative or binary... |
| adjLD | LD pruning of summary statistics |
| adjLDStat | Check concordance between marker effect and sparse LD matrix. |
| adjStat | Adjustment of marker summary statistics using clumping and... |
| adjustB | Adjust B-values |
| adjustMapLD | Adjust Linkage Disequilibrium (LD) Using Map Information |
| auc | Compute AUC |
| checkStat | Quality Control of Marker Summary Statistics |
| computeROC | Compute Receiver Operating Curve statistics |
| createLDsets | Create Linkage Disequilibrium (LD) Sets |
| gbayes | Bayesian linear regression models |
| gblup | Compute Genomic BLUP values |
| getG | Get elements from genotype matrix stored in PLINK bedfiles |
| getGRM | Extract elements from genomic relationship matrix (GRM)... |
| getLD | Retrieve Sparse LD Matrix for a Given Chromosome |
| getLDscores | Extract Linkage Disequilibrium (LD) Scores |
| getLDsets | Get marker LD sets |
| getMap | Retrieve the map for specified rsids on a given chromosome. |
| getMarkers | Retrieve marker rsids in a specified genome region. |
| getPos | Retrieve the positions for specified rsids on a given... |
| getSparseLD | Extract Sparse Linkage Disequilibrium (LD) Information |
| gfilter | Filter genetic marker data based on different quality... |
| glma | Single marker association analysis using linear models or... |
| gmap | Finemapping using Bayesian Linear Regression Models |
| gprep | Prepare genotype data for all statistical analyses |
| greml | Genomic rescticted maximum likelihood (GREML) analysis |
| grm | Computing the genomic relationship matrix (GRM) |
| gscore | Genomic scoring based on single marker summary statistics |
| gsea | Gene set enrichment analysis |
| gsim | Genomic simulation |
| gsimC | Simulate Genetic Data Based on Given Parameters |
| gsimR | Simulate Genetic Data Based on Given Parameters |
| gsolve | Solve linear mixed model equations |
| hwe | Perform Hardy Weinberg Equilibrium Test |
| ldsc | LD score regression |
| ldscore | Compute LD (Linkage Disequilibrium) Scores for a Given... |
| magma | Bayesian Multi-marker Analysis of Genomic Annotation... |
| mapSets | Map Sets to rsids |
| mapStat | Map marker summary statistics to Glist |
| mergeGRM | Merge multiple GRMlist objects |
| mtadj | Adjustment of marker effects using correlated trait... |
| plotBayes | Plot fit from gbayes |
| plotForest | Forest plot |
| plotLD | Plot LD Matrix |
| plotROC | Plot Receiver Operating Curves |
| pops | Bayesian Polygenic Prioritisation Scoring (Bayesian POPS) |
| predict_auc_mt_cc | Expected AUC for prediction of a binary trait using... |
| predict_auc_mt_continuous | Expected AUC for prediction of a binary trait using... |
| predict_auc_st | Expected AUC for prediction of a binary trait |
| predict_r2_mt | Expected R2 for multiple trait prediction of continuous... |
| predict_r2_st | Expected R2 for single trait prediction of a continuous trait |
| rnag | Compute Nagelkerke R2 |
| splitWithOverlap | Split Vector with Overlapping Segments |
| vegas | Perform VEGAS Gene-Based Association Analysis |
| writeBED | Write a subset of data from a BED file |
