Regression Methods for IBD Linkage with Covariates


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Documentation for package ‘ibdreg’ version 0.3.8

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align.ibd.var align ibd.var object with relative pairs within pairs.frame object
chibar3.w Compute mixture proportions, w, for mixture chi-square distribution
create.ibd.dat Create an ibd.dat object
create.pairs.frame create a data frame for relative pairs
create.pairs.frame.cvec create a data frame for relative pairs
exact.ibd.var create an ibd.var object
Ginv Compute Generalized Inverse of Input Matrix
ibd.df.merlin Create and return a data.frame with ibd data from merlin
ibd.moments calculate moments (mean, variance) for simulated ibd vectors
ibdreg Regression Methods to Test for Linkage With Covariates
linkage.all Linkage test statistics for ALL relative pairs
linkage.all.pedloop Linkage test statistics for ALL relative pairs
linkage.tests Linkage tests for relative pair groups
linkage.tests.B0 Linkage tests for relative pair groups
linkage.tests.pedloop Linkage tests for relative pair groups
lsConstrain.fit Minimize Inequality Constrained Mahalanobis Distance
mergeIBD Merge ibd and covariate data
minpRows find the rows of a data frame with the minimum pvalue
pairDiff Combine person-specific covariates to pair-specific
pairSum Combine person-specific covariates to pair-specific
pchibar cumulative probability of a chibar distribution
plot.ibdreg plot an ibdreg object
plot.ibdreg.unexpect Plot unconstrained and constrained linkage tests to indicate areas of unexpected allele sharing
plot.linkage.all Plot a linkage.all object
plot.linkage.tests Plot a linkage.tests object
plotpval Plot the -log10 of pvalues
print.ibd.var print an ibd.var object
print.ibdreg print and ibdreg object
print.linkage.all Print or summarize a linkage.all object
print.linkage.tests Print a linkage.tests object
printBanner Print a nice banner
resources track system resources
setFounderAlleles set-up functions for sim.mark.prop
sim.ibd.setup set-up functions for sim.mark.prop
sim.ibd.var Create an ibd.var object via simulations using gene-dropping
sim.mark.prop Simulate Marker Propagation