Man pages for jennasimit/flashfm
flexible and shared information fine-mapping

allC12internal function for calcAdjPP for that gives list of...
best.models.cppBest models from a snpmpd object by cpp or maximum number of...
betaList of vectors of single-SNP effects (GWAS) for two...
calcABFCalculate approximate Bayes' factor (ABF)
calcAdjPPCalculates trait-adjusted posterior probabilities for all...
calcCres12covariance between residuals of a pair of models for a trait...
calcD12internal function for calcAdjPP for the 2-trait case
calcDconinternal function for calcAdjPP that gives constant term for...
calc.maxmincalculate max or min of subset of a matrix
calcQ12internal function for calcAdjPP for a pair of traits
cor2covCorrelation Matrix to Covariance Matrix Conversion
cor.refdata.fnThin genotype correlation matrix for JAM input
covYCovariance matrix for two simulated traits
cvsVector of rsids for causal variants of two simulated traits
expand.modinternal function for expanding models by tag SNPs in...
flashfmMarginal PP for models of a set of traits, sharing...
flashfm.inputKey input for flashfm - constructs snpmod object list and...
FLASHFMwithJAMWrapper to run single-trait fine-mapping with...
fmOutput from running FLASHFMwithJAM on the simulated dataset...
FMconfigList of FINEMAP config file contents for two simulated traits
FMtablesFormats flashfm output to table format
groupIDs.fnFind SNP group ids for a set of SNPs
groupmultiGroup SNPs; adapted from group.multi of...
JAMexpandedCor.multiExpanded version of JAM (a single-trait fine-mapping...
JAMexpanded.multiExpanded version of JAM (a single-trait fine-mapping...
JAMmain.inputOutput from JAMexpanded.multi for two simulated traits
JAM_PointEstimatesinternal function for multibeta, modified from...
JAM_PointEstimates_Xcovinternal function for multibeta, modified from...
logsumlogsum
makemodinternal function makemod from GUESSFM
makeNlistSample size information needed for flashfm
makeNlist.relSample size information needed for flashfm, when samples are...
makeplinkConvert genotype score data to plink ped-map format
makeSNPgroupsMake SNP groups using fine-mapping information from all of...
makeSNPgroups2Make two sets of SNP groups using fine-mapping information...
marginalppMarginal PP for models sharing information between traits
marg.snpsinternal function marg.snps from GUESSFM
marg.snps.vecsinternal function marg.snps.vec from GUESSFM
mod.fninternal processing function for JAMexpanded.multi
multibetaUsing summary statistics, calculates joint effect estimates
NVector of samples sizes for two simulated traits
NeffApproximate effective sample size from GWAS of related...
PPsummariseSummarise PP and MPP results from single-trait fine-mapping...
prune_maximalinternal function for ref.data.fn
rafVector of RAFs from the simulated genotype matrix X used to...
refdata.fnThin genotype matrix for JAM input
score2allelesinternal function for makeplink
snpinfoDetails of SNPs from the simulated genotype matrix X used to...
summaryStatsSummary statistics needed for flashfm input
Sxy.hatestimates cross-product of each SNP with one trait
tagexpand.modinternal function for expanding models by tag SNPs in...
Vres.allvariance of model residuals for trait T1 at all models that...
Vres.hatvariance of model residuals for trait T1 at model index imod
Vx.hatInternal function, Vx.hat
XSimulated genotype matrix used to generate two traits
ybarMean vector for two simulated traits
jennasimit/flashfm documentation built on July 23, 2021, 4:10 a.m.