R: Regression Methods for IBD Linkage with Covariates

# Regression Methods for IBD Linkage with Covariates

## Documentation for package ‘ibdreg’ version 0.3.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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