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ibdreg (version 0.1.2)

Regression Methods for IBD Linkage With Covariates

Description

A method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.

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Version

Install

install.packages('ibdreg')

Monthly Downloads

103

Version

0.1.2

License

GPL-2 | file LICENSE

Maintainer

Jason Sinnwell

Last Published

December 9th, 2023

Functions in ibdreg (0.1.2)

print.ibd.var

print an ibd.var object
print.linkage.all

Print or summarize a linkage.all object
create.ibd.dat

Create an ibd.dat object
print.ibdreg

print and ibdreg object
sim.mark.prop

Simulate Marker Propagation
ibdreg

Regression Methods to Test for Linkage With Covariates
plotpval

Plot the -log10 of pvalues
print.linkage.tests

Print a linkage.tests object
plot.linkage.tests

Plot a linkage.tests object
plot.ibdreg

plot an ibdreg object
exact.ibd.var

create an ibd.var object
create.pairs.frame

create a data frame for relative pairs
linkage.tests

Linkage tests for relative pair groups
linkage.all

Linkage test statistics for ALL relative pairs
lsConstrain.fit

Minimize Inequality Constrained Mahalanobis Distance
sim.ibd.setup

set-up functions for sim.mark.prop
sr.strsplit

Split a vector of strings by a single character
mergeIBD

Merge ibd and covariate data
align.ibd.var

align ibd.var object with relative pairs within pairs.frame object
sim.ibd.var

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

Compute Generalized Inverse of Input Matrix
pchibar

cumulative probability of a chibar distribution
ibd.moments

calculate moments (mean, variance) for simulated ibd vectors
pairSum

Combine person-specific covariates to pair-specific
plot.linkage.all

Plot a linkage.all object
plot.ibdreg.unexpect

Plot unconstrained and constrained linkage tests to indicate areas of unexpected allele sharing
chibar3.w

Compute mixture proportions, w, for mixture chi-square distribution
resources

track system resources
sr.class

Return or set the class attribute of an object, compatible for both R and S-PLUS
printBanner

Print a nice banner
ibd.df.merlin

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

find the rows of a data frame with the minimum pvalue