ibdreg: Regression Methods for IBD Linkage With Covariates

Share:

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.

Author
Jason P. Sinnwell and Daniel J. Schaid
Date of publication
2013-04-20 07:47:38
Maintainer
Jason P. Sinnwell <Sinnwell.Jason@mayo.edu>
License
GPL-2 | file LICENSE
Version
0.2.5
URLs

View on CRAN

Man pages

align.ibd.var
align ibd.var object with relative pairs within pairs.frame...
chibar3.w
Compute mixture proportions, w, for mixture chi-square...
create.ibd.dat
Create an ibd.dat object
create.pairs.frame
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.tests
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
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...
plot.linkage.all
Plot a linkage.all object
plot.linkage.tests
Plot a linkage.tests object
plotpval
Plot the -log10 of pvalues
printBanner
Print a nice banner
print.ibdreg
print and ibdreg object
print.ibd.var
print an ibd.var object
print.linkage.all
Print or summarize a linkage.all object
print.linkage.tests
Print a linkage.tests object
resources
track system resources
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

Files in this package

ibdreg
ibdreg/MD5
ibdreg/DESCRIPTION
ibdreg/LICENSE
ibdreg/man
ibdreg/man/printBanner.Rd
ibdreg/man/mergeIBD.Rd
ibdreg/man/sim.mark.prop.Rd
ibdreg/man/ibdreg.Rd
ibdreg/man/plot.linkage.all.Rd
ibdreg/man/lsConstrain.fit.Rd
ibdreg/man/print.ibd.var.Rd
ibdreg/man/plot.ibdreg.Rd
ibdreg/man/align.ibd.var.Rd
ibdreg/man/pchibar.Rd
ibdreg/man/resources.Rd
ibdreg/man/plot.linkage.tests.Rd
ibdreg/man/create.ibd.dat.Rd
ibdreg/man/plot.ibdreg.unexpect.Rd
ibdreg/man/linkage.all.Rd
ibdreg/man/sim.ibd.var.Rd
ibdreg/man/pairSum.Rd
ibdreg/man/print.linkage.tests.Rd
ibdreg/man/ibd.moments.Rd
ibdreg/man/print.ibdreg.Rd
ibdreg/man/chibar3.w.Rd
ibdreg/man/Ginv.Rd
ibdreg/man/ibd.df.merlin.Rd
ibdreg/man/exact.ibd.var.Rd
ibdreg/man/create.pairs.frame.Rd
ibdreg/man/plotpval.Rd
ibdreg/man/print.linkage.all.Rd
ibdreg/man/sim.ibd.setup.Rd
ibdreg/man/linkage.tests.Rd
ibdreg/man/minpRows.Rd
ibdreg/src
ibdreg/src/sim.mark.prop.c
ibdreg/src/lsConstrain.c
ibdreg/src/mcmemory.h
ibdreg/perl
ibdreg/perl/exact.ibd.var.pl
ibdreg/perl/merlin.post.ibd.pl
ibdreg/perl/merlin.prior.ibd.pl
ibdreg/perl/gws.merlin.ibd.pl
ibdreg/inst
ibdreg/inst/NEWS.Rd
ibdreg/inst/doc
ibdreg/inst/doc/manualIBDReg.pdf
ibdreg/inst/doc/GPL.txt
ibdreg/R
ibdreg/R/print.linkage.all.q
ibdreg/R/create.pairs.frame.cvec.q
ibdreg/R/resources.q
ibdreg/R/linkage.all.pedloop.q
ibdreg/R/plot.ibdreg.unexpect.q
ibdreg/R/Ginv.R
ibdreg/R/create.pairs.frame.q
ibdreg/R/zzz.ibdreg.q
ibdreg/R/print.ibdreg.q
ibdreg/R/plot.linkage.all.q
ibdreg/R/pairSum.q
ibdreg/R/linkage.tests.B0.q
ibdreg/R/setFounderAlleles.q
ibdreg/R/minpRows.q
ibdreg/R/mergeIBD.q
ibdreg/R/linkage.tests.q
ibdreg/R/plot.ibdreg.q
ibdreg/R/sim.mark.prop.q
ibdreg/R/lsConstrain.fit.q
ibdreg/R/ibdreg.q
ibdreg/R/sim.ibd.setup.q
ibdreg/R/align.ibd.var.q
ibdreg/R/linkage.tests.pedloop.q
ibdreg/R/exact.ibd.var.q
ibdreg/R/ibd.df.merlin.q
ibdreg/R/print.ibd.var.q
ibdreg/R/printBanner.q
ibdreg/R/create.ibd.dat.q
ibdreg/R/print.linkage.tests.q
ibdreg/R/pchibar.q
ibdreg/R/plot.linkage.tests.q
ibdreg/R/pairDiff.q
ibdreg/R/sim.ibd.var.q
ibdreg/R/chibar3.w.q
ibdreg/R/linkage.all.q
ibdreg/R/ibd.moments.q
ibdreg/R/plotpval.q
ibdreg/NAMESPACE