Function reference • flashfm

All functions
`FLASHFMwithFINEMAP()`	Wrapper to run single-trait fine-mapping with FINEMAP on each trait, followed by flashfm and then constuct SNP groups for each approach and summarises results
`FLASHFMwithJAM()`	Wrapper to run single-trait fine-mapping with JAMexpandedCor.multi on each trait, followed by flashfm and then constuct SNP groups for each approach and summarises results
`FLASHFMwithJAMhat()`	Wrapper to run single-trait fine-mapping with JAMexpandedCor.multi on each trait, followed by flashfm (using fast approximation version) and then constuct SNP groups for each approach and summarises results
`FMconfig`	List of FINEMAP config file contents for two simulated traits
`FMtables()`	Formats flashfm output to table format
`JAM_PointEstimates()`	internal function for multibeta, modified from JAM_PointEstimates_Package_Simplified of R2BGLiMS package (Paul Newcombe)
`JAM_PointEstimates_Xcov()`	internal function for multibeta, modified from JAM_PointEstimates_Package_Simplified of R2BGLiMS package
`JAMexpanded.multi()`	Expanded version of JAM (a single-trait fine-mapping approach) that first runs on thinned SNPs and then expands models on tag SNPs; this can run independently on multiple traits
`JAMexpandedCor.multi()`	Expanded version of JAM (a single-trait fine-mapping approach) that first runs on thinned SNPs and then expands models on tag SNPs; this can run independently on multiple traits
`JAMexpandedCor.multi2()`	Expanded version of JAM (a single-trait fine-mapping approach) that first runs on thinned SNPs and then expands models on tag SNPs; this can run independently on multiple traits This version is more stable than JAMexpandedCor.multi, but slower, so is run only if JAMexpandedCor.multi fails
`JAMmain.input`	Output from JAMexpanded.multi for two simulated traits
`N`	Vector of samples sizes for two simulated traits
`Neff()`	Approximate effective sample size from GWAS of related samples
`PPsummarise()`	Summarise PP and MPP results from single-trait fine-mapping and flashfm, by SNP and by SNP group
`Sxy.hat()`	estimates cross-product of each SNP with one trait
`Vres.all()`	variance of model residuals for trait T1 at all models that have joint effect estimates
`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
`snps()` `tags()`	Accessors for groups objects
`allC12()`	internal function for calcAdjPP for that gives list of covariance matrix of residuals for all trait pairs
`allcredsets()`	Construct a credible set for each trait and under each of single and multi-trait fine-mapping
`best.models.cpp()`	Best models from a snpmpd object by cpp or maximum number of models - modification of best.models from GUESSFM by Chris Wallace
`best.snps()`	Best SNPs
`beta`	List of vectors of single-SNP effects (GWAS) for two simulated traits
`calc.maxmin()`	calculate max or min of subset of a matrix
`calcABF()`	Calculate approximate Bayes' factor (ABF)
`calcAdjPP()`	Calculates trait-adjusted posterior probabilities for all traits at sharing parameter kappa
`calcCres12()`	covariance between residuals of a pair of models for a trait pair
`calcD12()`	internal function for calcAdjPP for the 2-trait case
`calcDcon()`	internal function for calcAdjPP that gives constant term for delta
`calcQ12()`	internal function for calcAdjPP for a pair of traits
`convert()`	Convert from old definitions of groups, tags classes to new
`cor.refdata.fn()`	Thin genotype correlation matrix for JAM input
`cor2cov()`	Correlation Matrix to Covariance Matrix Conversion
`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 JAMexpanded.multi
`finemap()`	Wrapper to run FINEMAP (Benner et al. 2016) in R
`flashfm()`	Marginal PP for models of a set of traits, sharing information between the traits
`flashfm.input()`	Key input for flashfm - constructs snpmod object list and joint effect estimates list for all trait if have external single trait fine-mapping results
`fm`	Output from running FLASHFMwithJAM on the simulated dataset in this package
`fm2`	Output from FLASHFMwithFINEMAP for two simulated traits
`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 SNPs defined by their mutual LD
`tagsof()` `taggedby()` `[`(<groups>,<character>,<missing>,<missing>) `[`(<groups>,<numeric>,<missing>,<missing>) `[`(<groups>,<logical>,<missing>,<missing>) `[`(<tags>,<character>,<missing>,<missing>) `[[`(<groups>,<numeric>) `[[`(<groups>,<logical>) `[[`(<groups>,<character>)	`tagsof` shows tags for a named character vector of SNPs
`gwas.list`	List of GWAS data.frames for each of the two simulated traits; format of z files of FINEMAP
`logsum()`	logsum
`makeNlist()`	Sample size information needed for flashfm
`makeNlist.rel()`	Sample size information needed for flashfm, when samples are related and have effective sample sizes for each trait
`makeSNPgroups()`	Make SNP groups using fine-mapping information from all of the traits
`makeSNPgroups2()`	Make two sets of SNP groups using fine-mapping information from all of the traits using two sets of results and maps the names between them
`makemod()`	internal function makemod
`makeplink()`	Convert genotype score data to plink ped-map format
`marg.snps()`	internal function marg.snps
`marg.snps.vecs()`	internal function marg.snps.vec
`marginalpp()`	Marginal PP for models sharing information between traits
`mod.fn()`	internal processing function for JAMexpanded.multi
`multibeta()`	Using summary statistics, calculates joint effect estimates
`overlap()`	overlap
`ppnsnp-class`	Class to hold results of pp.nsnp
`prune_maximal()`	internal function for ref.data.fn
`raf`	Vector of RAFs from the simulated genotype matrix X used to generate two traits
`refdata.fn()`	Thin genotype matrix for JAM input
`score2alleles()`	internal function for makeplink
`show(<snpmod>)` `show(<snppicker>)` `show(<ppnsnp>)` `show(<tags>)` `show(<groups>)`	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 generate two traits
`snpmod-class`	Class to hold data relating to multiple models fitted to SNP data
`snppicker-class`	Class to hold results of snp.picker algorithm
`summary(<snppicker>)` `summary(<groups>)`	Summaries
`summaryStats()`	Summary statistics needed for flashfm input
`tag()`	tag
`tagexpand.mod()`	internal function for expanding models by tag SNPs in JAMexpandedCor.multi
`tags-class`	Tags focused class for holding information about sets of SNPs defined by their mutual LD
`union()`	Create a union of groups, snppicker or tags objects
`ybar`	Mean vector for two simulated traits

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