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ibdreg

Regression Methods for IBD Linkage with Covariates. A method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs, accounting for correlations of IBD statistics and covariates for relative pairs within the same pedigree.

Authors

Daniel J. Schaid and Jason P. Sinnwell

Notes

Prefer to keep pdf version of manual, so borrowed this suggestion to embed into a manual that can be manual that can be indexed like other vignettes.

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Version

Install

install.packages('ibdreg')

Monthly Downloads

211

Version

0.3.8

License

GPL-2 | file LICENSE

Maintainer

Jason Sinnwell

Last Published

December 8th, 2023

Functions in ibdreg (0.3.8)

pairSum

Combine person-specific covariates to pair-specific
plot.ibdreg

plot an ibdreg object
minpRows

find the rows of a data frame with the minimum pvalue
pchibar

cumulative probability of a chibar distribution
plot.ibdreg.unexpect

Plot unconstrained and constrained linkage tests to indicate areas of unexpected allele sharing
linkage.tests

Linkage tests for relative pair groups
mergeIBD

Merge ibd and covariate data
lsConstrain.fit

Minimize Inequality Constrained Mahalanobis Distance
plot.linkage.tests

Plot a linkage.tests object
plot.linkage.all

Plot a linkage.all object
sim.mark.prop

Simulate Marker Propagation
sim.ibd.setup

set-up functions for sim.mark.prop
resources

track system resources
printBanner

Print a nice banner
sim.ibd.var

Create an ibd.var object via simulations using gene-dropping
plotpval

Plot the -log10 of pvalues
print.linkage.tests

Print a linkage.tests object
print.ibd.var

print an ibd.var object
print.ibdreg

print and ibdreg object
print.linkage.all

Print or summarize a linkage.all object
Ginv

Compute Generalized Inverse of Input Matrix
create.ibd.dat

Create an ibd.dat object
exact.ibd.var

create an ibd.var object
ibd.df.merlin

Create and return a data.frame with ibd data from merlin
ibd.moments

calculate moments (mean, variance) for simulated ibd vectors
chibar3.w

Compute mixture proportions, w, for mixture chi-square distribution
create.pairs.frame

create a data frame for relative pairs
align.ibd.var

align ibd.var object with relative pairs within pairs.frame object
linkage.all

Linkage test statistics for ALL relative pairs
ibdreg

Regression Methods to Test for Linkage With Covariates