GCA-package: GCA: Genetic connectedness analysis
In HaipengU/GCA2: Genetic Connectedness Analysis

Description Details Available functions in GCA package Author(s) References

An R package for genetic connectedness analysis across units using pedigree and genomic data.

The GCA package encompasses numerous connectedness statistics, which could be labeled as two groups, by reference to connectedness based on prediction error variance (PEV) and variance of unit effect estimates (VE). The PEV-derived metrics include prediction error variance of differences (PEVD), coefficient of determination (CD), and prediction error correlation (r). These PEV-derived metrics can be summarized at the unit level as the average PEV within and across units (GrpAve), average PEV of all pairwise differences between individuals across units (IdAve), or using a contrast vector (Contrast). VE-derived metrics comprise variance of differences in management unit effects (VED), coefficient of determination of VED (CDVED), and connectedness rating (CR). Three correction factors accounting for the number of fixed effects can be applied for each VE-derived metric. These include non-correction (0), correction of unit effect (1), and correction of two or more fixed effects (2). The core function of GCA is integrated with C++ to improve computational efficiency using the Rcpp package (Eddelbuettel and François 2011). The details of these connectedness statistics can be found in Yu and Morota 2019.

computeA(): Computation of numerator relationship matrix.
computeG(): Computation of genomic relationship matrix.
gca(): Measures of genetic connectedness.
varcomp(): Estimates of variance components using eigenvalues and eigenvectors.

Haipeng Yu and Gota Morota

Maintainer: Haipeng Yu haipengyu@vt.edu

Eddelbuettel D, François R (2011). Rcpp: Seamless R and C++ Integration. Journal of Statistical Software, 40(8), 1–18.

Yu H and Morota G. 2019. GCA: An R Package for Genetic Connectedness Analysis Using Pedigree and Genomic Data.

HaipengU/GCA2 documentation built on March 1, 2021, 7:41 a.m.