Regression Methods for IBD Linkage with Covariates
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Documentation for package ‘ibdreg’ version 0.3.8
Help Pages
| align.ibd.var | align ibd.var object with relative pairs within pairs.frame object |
| chibar3.w | Compute mixture proportions, w, for mixture chi-square distribution |
| create.ibd.dat | Create an ibd.dat object |
| create.pairs.frame | create a data frame for relative pairs |
| create.pairs.frame.cvec | 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.all.pedloop | Linkage test statistics for ALL relative pairs |
| linkage.tests | Linkage tests for relative pair groups |
| linkage.tests.B0 | Linkage tests for relative pair groups |
| linkage.tests.pedloop | 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 |
| pairDiff | Combine person-specific covariates to pair-specific |
| 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 areas of unexpected allele sharing |
| plot.linkage.all | Plot a linkage.all object |
| plot.linkage.tests | Plot a linkage.tests object |
| plotpval | Plot the -log10 of pvalues |
| print.ibd.var | print an ibd.var object |
| print.ibdreg | print and ibdreg object |
| print.linkage.all | Print or summarize a linkage.all object |
| print.linkage.tests | Print a linkage.tests object |
| printBanner | Print a nice banner |
| resources | track system resources |
| setFounderAlleles | set-up functions for sim.mark.prop |
| 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 |