flexible and shared information fine-mapping

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**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**Browse all...**

marg.snps | R Documentation |

internal function marg.snps

marg.snps(d)

`d` |
snpmod object |

Chris Wallace

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