Package: RepeatABEL 2.0

Lars Ronnegard

RepeatABEL: GWAS for Multiple Observations on Related Individuals

Performs genome-wide association studies (GWAS) on individuals that are both related and have repeated measurements. For each Single Nucleotide Polymorphism (SNP), it computes score statistic based p-values for a linear mixed model including random polygenic effects and a random effect for repeated measurements. The computed p-values can be visualized in a Manhattan plot. For more details see Ronnegard et al. (2016) <doi:10.1111/2041-210X.12535> and for more examples see <https://github.com/larsronn/RepeatABEL_Tutorials>.

Authors:Lars Ronnegard [aut, cre]

RepeatABEL_2.0.tar.gz
RepeatABEL_2.0.tar.gz(r-4.7-any)RepeatABEL_2.0.tar.gz(r-4.6-any)
RepeatABEL_2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RepeatABEL/json (API)
NEWS

# Install 'RepeatABEL' in R:

install.packages('RepeatABEL', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.26 score 1 stars 18 scripts 445 downloads 12 exports 6 dependencies

Last updated from:7541db3ce1. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	118
source / vignettes	OK	215
linux-release-x86_64	OK	121
wasm-release	OK	94

Exports:chromosome compute.GRM constructV Create_gwaa_data2 Create_gwaa_scan2 estlambda idnames nids preFitModel rGLS simulate_gendata simulate_PhenData

Dependencies:hglm hglm.data lattice MASS Matrix sp

Help page	Topics
Extracts the chromosome numbers	chromosome
Computes a Genetic Relationship Matrix from a GenABEL-like object	compute.GRM
Constructs the (co)variance matrix for y	constructV
Creates a gwaa.data2 object	Create_gwaa_data2
Creates a scan.gwaa2 object	Create_gwaa_scan2
Function to estimate lambda	estlambda
An S4 class to represent GWAS input data	gwaa.data2-class
Extracts the id names	idnames
A function to subset an gwaa.data2 object	keep_gwaa_data
Extracts the map information	map
Extracts the number of ids	nids
Function to plot P-values as a Manhattan plot	plot.scan.gwaa2
Fits a linear mixed model (without fixed SNP effects) and computes the fitted variance-covariance matrix for later use in the rGLS function.	preFitModel
GWAS for Studies having Repeated Measurements on Related Individuals	rGLS
An S4 class to represent SNP data	scan.gwaa2-class
Function to simulate genotype data for the RepeatABEL package.	simulate_gendata
Simulation function for the RepeatABEL package.	simulate_PhenData
Imputes column means to missing genotypes	SmoothSNPmatrix
An S4 class to represent SNP data	snp.data
Extracts the snpnames	snpnames
Summary function for the rGLS output	summary.scan.gwaa2

Package: RepeatABEL 2.0

RepeatABEL: GWAS for Multiple Observations on Related Individuals

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)