flexible and shared information fine-mapping

allC12 | internal function for calcAdjPP for that gives list of... |

best.models.cpp | Best models from a snpmpd object by cpp or maximum number of... |

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 |

cor2cov | Correlation Matrix to Covariance Matrix Conversion |

cor.refdata.fn | Thin genotype correlation matrix for JAM input |

covY | Covariance matrix for two simulated traits |

cvs | Vector of rsids for causal variants of two simulated traits |

expand.mod | internal function for expanding models by tag SNPs in... |

flashfm | Marginal PP for models of a set of traits, sharing... |

flashfm.input | Key input for flashfm - constructs snpmod object list and... |

FLASHFMwithJAM | Wrapper to run single-trait fine-mapping with... |

fm | Output from running FLASHFMwithJAM on the simulated dataset... |

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 of... |

JAMexpandedCor.multi | 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 from GUESSFM |

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 from GUESSFM |

marg.snps.vecs | internal function marg.snps.vec from GUESSFM |

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... |

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 |

snpinfo | Details of SNPs from the simulated genotype matrix X used to... |

summaryStats | Summary statistics needed for flashfm input |

Sxy.hat | estimates cross-product of each SNP with one trait |

tagexpand.mod | internal function for expanding models by tag SNPs in... |

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 |

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