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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