| accessors | Accessors for groups objects |
| allC12 | internal function for calcAdjPP for that gives list of... |
| allcredsets | Construct a credible set for each trait and under each of... |
| best.models.cpp | Best models from a snpmpd object by cpp or maximum number of... |
| best.snps | Best SNPs |
| beta | List of vectors of single-SNP effects (GWAS) for two... |
| calcABF | Calculate approximate Bayes' factor (ABF) |
| calcAdjPP | Calculates trait-adjusted posterior probabilities for all... |
| calcCres12 | covariance between residuals of a pair of models for a trait... |
| calcD12 | internal function for calcAdjPP for the 2-trait case |
| calcDcon | internal function for calcAdjPP that gives constant term for... |
| calc.maxmin | calculate max or min of subset of a matrix |
| calcQ12 | internal function for calcAdjPP for a pair of traits |
| conversion | Convert from old definitions of groups, tags classes to new |
| cor2cov | Correlation Matrix to Covariance Matrix Conversion |
| cor.refdata.fn | Thin genotype correlation matrix for JAM input |
| covY | Covariance matrix for two simulated traits |
| credset | Construct a credible set for a trait |
| cvs | Vector of rsids for causal variants of two simulated traits |
| expand.mod | internal function for expanding models by tag SNPs in... |
| finemap | Wrapper to run FINEMAP (Benner et al. 2016) in R |
| flashfm | Marginal PP for models of a set of traits, sharing... |
| flashfm.input | Key input for flashfm - constructs snpmod object list and... |
| FLASHFMwithFINEMAP | Wrapper to run single-trait fine-mapping with FINEMAP on each... |
| FLASHFMwithJAM | Wrapper to run single-trait fine-mapping with... |
| FLASHFMwithJAMhat | Wrapper to run single-trait fine-mapping with... |
| fm | Output from running FLASHFMwithJAM on the simulated dataset... |
| fm2 | Output from FLASHFMwithFINEMAP for two simulated traits |
| FMconfig | List of FINEMAP config file contents for two simulated traits |
| FMtables | Formats flashfm output to table format |
| groupIDs.fn | Find SNP group ids for a set of SNPs |
| groupmulti | Group SNPs; adapted from group.multi by Chris Wallace |
| groups-class | Group focused class for holding information about sets of... |
| groups-subset | 'tagsof' shows tags for a named character vector of SNPs |
| gwas.list | List of GWAS data.frames for each of the two simulated... |
| JAMexpandedCor.multi | Expanded version of JAM (a single-trait fine-mapping... |
| JAMexpandedCor.multi2 | Expanded version of JAM (a single-trait fine-mapping... |
| JAMexpanded.multi | Expanded version of JAM (a single-trait fine-mapping... |
| JAMmain.input | Output from JAMexpanded.multi for two simulated traits |
| JAM_PointEstimates | internal function for multibeta, modified from... |
| JAM_PointEstimates_Xcov | internal function for multibeta, modified from... |
| logsum | logsum |
| makemod | internal function makemod |
| makeNlist | Sample size information needed for flashfm |
| makeNlist.rel | Sample size information needed for flashfm, when samples are... |
| makeplink | Convert genotype score data to plink ped-map format |
| makeSNPgroups | Make SNP groups using fine-mapping information from all of... |
| makeSNPgroups2 | Make two sets of SNP groups using fine-mapping information... |
| marginalpp | Marginal PP for models sharing information between traits |
| marg.snps | internal function marg.snps |
| marg.snps.vecs | internal function marg.snps.vec |
| mod.fn | internal processing function for JAMexpanded.multi |
| multibeta | Using summary statistics, calculates joint effect estimates |
| N | Vector of samples sizes for two simulated traits |
| Neff | Approximate effective sample size from GWAS of related... |
| overlap | overlap |
| ppnsnp-class | Class to hold results of pp.nsnp |
| PPsummarise | Summarise PP and MPP results from single-trait fine-mapping... |
| prune_maximal | internal function for ref.data.fn |
| raf | Vector of RAFs from the simulated genotype matrix X used to... |
| refdata.fn | Thin genotype matrix for JAM input |
| score2alleles | internal function for makeplink |
| show-methods | Show |
| snpin | Check whether a snp is in a snppicker, groups or tags object |
| snpinfo | Details of SNPs from the simulated genotype matrix X used to... |
| snpmod-class | Class to hold data relating to multiple models fitted to SNP... |
| snppicker-class | Class to hold results of snp.picker algorithm |
| summary | Summaries |
| summaryStats | Summary statistics needed for flashfm input |
| Sxy.hat | estimates cross-product of each SNP with one trait |
| tag | tag |
| tagexpand.mod | internal function for expanding models by tag SNPs in... |
| tags-class | Tags focused class for holding information about sets of SNPs... |
| union | Create a union of groups, snppicker or tags objects |
| Vres.all | variance of model residuals for trait T1 at all models that... |
| Vres.hat | variance of model residuals for trait T1 at model index imod |
| Vx.hat | Internal function, Vx.hat |
| X | Simulated genotype matrix used to generate two traits |
| ybar | Mean vector for two simulated traits |
