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ibdreg (version 0.1.3)

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

0.1.3

License

GPL-2 | file LICENSE

Maintainer

Jason Sinnwell

Last Published

October 29th, 2012

Functions in ibdreg (0.1.3)

print.ibd.var

print an ibd.var object
chibar3.w

Compute mixture proportions, w, for mixture chi-square distribution
ibd.moments

calculate moments (mean, variance) for simulated ibd vectors
sim.ibd.var

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

Create an ibd.dat object
lsConstrain.fit

Minimize Inequality Constrained Mahalanobis Distance
Ginv

Compute Generalized Inverse of Input Matrix
linkage.all

Linkage test statistics for ALL relative pairs
align.ibd.var

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

Print or summarize a linkage.all object
exact.ibd.var

create an ibd.var object
plot.linkage.all

Plot a linkage.all object
create.pairs.frame

create a data frame for relative pairs
minpRows

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

Combine person-specific covariates to pair-specific
ibd.df.merlin

Create and return a data.frame with ibd data from merlin
print.linkage.tests

Print a linkage.tests object
mergeIBD

Merge ibd and covariate data
plot.ibdreg

plot an ibdreg object
sim.ibd.setup

set-up functions for sim.mark.prop
plotpval

Plot the -log10 of pvalues
sr.class

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

Linkage tests for relative pair groups
resources

track system resources
ibdreg

Regression Methods to Test for Linkage With Covariates
plot.ibdreg.unexpect

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

Split a vector of strings by a single character
print.ibdreg

print and ibdreg object
pchibar

cumulative probability of a chibar distribution
plot.linkage.tests

Plot a linkage.tests object
printBanner

Print a nice banner
sim.mark.prop

Simulate Marker Propagation