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. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.

AuthorJason P. Sinnwell and Daniel J. Schaid
Date of publication2013-04-20 07:47:38
MaintainerJason P. Sinnwell <Sinnwell.Jason@mayo.edu>
LicenseGPL-2 | file LICENSE
Version0.2.5
http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

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

Functions

align.ibd.var Man page
chibar3.w Man page
create.ibd.dat Man page
create.pairs.frame Man page
create.pairs.frame.cvec Man page
exact.ibd.var Man page
Ginv Man page
ibd.df.merlin Man page
ibd.moments Man page
ibdreg Man page
linkage.all Man page
linkage.all.pedloop Man page
linkage.tests Man page
linkage.tests.B0 Man page
linkage.tests.pedloop Man page
lsConstrain.fit Man page
mergeIBD Man page
minpRows Man page
pairDiff Man page
pairSum Man page
pchibar Man page
plot.ibdreg Man page
plot.ibdreg.unexpect Man page
plot.linkage.all Man page
plot.linkage.tests Man page
plotpval Man page
printBanner Man page
print.ibdreg Man page
print.ibd.var Man page
print.linkage.all Man page
print.linkage.tests Man page
resources Man page
setFounderAlleles Man page
sim.ibd.setup Man page
sim.ibd.var Man page
sim.mark.prop Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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