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ibdreg (version 0.1.1)

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

0.1.1

License

Copyright 2003 Mayo Foundation for Medical Education and Research. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the GPL license, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. For other licensing arrangements, please contact Daniel J. Schaid. Daniel J. Schaid, Ph.D. Division of Biostatistics Harwick Building Room 775 Mayo Clinic 200 First St., SW Rochester, MN 55905. Phone: 507-284-0639 fax: 507-284-9542 email: schaid@mayo.edu.

Maintainer

Jason Sinnwell

Last Published

December 9th, 2023

Functions in ibdreg (0.1.1)

Ginv

Compute Generalized Inverse of Input Matrix
align.ibd.var

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

create a data frame for relative pairs
chibar3.w

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

Create an ibd.var object via simulations using gene-dropping
print.linkage.all

Print or summarize a linkage.all object
pairSum

Combine person-specific covariates to pair-specific
lsConstrain.fit

Minimize Inequality Constrained Mahalanobis Distance
pchibar

cumulative probability of a chibar distribution
plot.ibdreg.unexpect

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

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

Print a nice banner
sim.ibd.setup

set-up functions for sim.mark.prop
ibdreg

Regression Methods to Test for Linkage With Covariates
print.linkage.tests

Print a linkage.tests object
print.ibdreg

print and ibdreg object
sr.strsplit

Split a vector of strings by a single character
minpRows

find the rows of a data frame with the minimum pvalue
plot.ibdreg

plot an ibdreg object
linkage.all

Linkage test statistics for ALL relative pairs
create.ibd.dat

Create an ibd.dat object
mergeIBD

Merge ibd and covariate data
plotpval

Plot the -log10 of pvalues
ibd.df.merlin

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

print an ibd.var object
plot.linkage.all

Plot a linkage.all object
plot.linkage.tests

Plot a linkage.tests object
ibd.moments

calculate moments (mean, variance) for simulated ibd vectors
linkage.tests

Linkage tests for relative pair groups
sim.mark.prop

Simulate Marker Propagation
exact.ibd.var

create an ibd.var object