flexible and shared information fine-mapping

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 |

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