| Type: | Package |
| Title: | Genotypic Variance Components |
| Version: | 0.4.0 |
| Maintainer: | Muhammad Yaseen <myaseen208@gmail.com> |
| Description: | Functionalities to compute model based genetic components i.e. genotypic variance, phenotypic variance and heritability for given traits of different genotypes from replicated data using methodology explained by Burton, G. W. & Devane, E. H. (1953) (<doi:10.2134/agronj1953.00021962004500100005x>) and Allard, R.W. (2010, ISBN:8126524154). |
| Depends: | R (≥ 3.2.3) |
| Imports: | dplyr, eda4treeR, lme4, magrittr, rlang, stats, supernova, tibble, R6 |
| License: | GPL-3 |
| URL: | https://myaseen208.com/gvcR/ https://github.com/MYaseen208/gvcR |
| BugReports: | https://github.com/myaseen208/gvcR/issues |
| RoxygenNote: | 7.3.2 |
| Encoding: | UTF-8 |
| Suggests: | testthat |
| NeedsCompilation: | no |
| Packaged: | 2024-09-30 21:23:22 UTC; myaseen208 |
| Author: | Muhammad Yaseen [aut, cre], Sami Ullah [aut, ctb] |
| Repository: | CRAN |
| Date/Publication: | 2024-10-01 06:50:02 UTC |
Genotypic Variance
Description
The 'gvc' class calculates genotypic variance, phenotypic variance, and broad-sense heritability from replicated data.
Details
The 'gvc' class uses methods explained by Burton, G. W. & Devane, E. H. (1953) and Allard, R.W. (2010). It includes methods for calculating genetic variance, phenotypic variance, and heritability.
Public fields
dataA 'tibble' containing the data for analysis.
yThe name of the response variable.
xThe name of the covariate (optional).
repThe name of the replicate factor.
genThe name of the genotype factor.
envThe name of the environmental factor.
Methods
Public methods
Method new()
Initialize the 'gvc' class with the data and variable names.
Usage
gvc$new(.data, .y, .x = NULL, .rep, .gen, .env)
Arguments
.dataA 'data.frame' containing the data for analysis.
.yThe response variable.
.xThe covariate (optional).
.repThe replicate factor.
.genThe genotype factor.
.envThe environmental factor.
Returns
An instance of the 'gvc' class.
Method calculate_gvar()
Calculate genetic variance.
Usage
gvc$calculate_gvar()
Returns
A list with the genetic variance ('gvar').
Method calculate_pvar()
Calculate phenotypic variance.
Usage
gvc$calculate_pvar()
Returns
A list with the phenotypic variance ('pvar').
Method calculate_herit()
Calculate broad-sense heritability.
Usage
gvc$calculate_herit()
Returns
A list with the heritability ('h2').
Method clone()
The objects of this class are cloneable with this method.
Usage
gvc$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
df1 <- data.frame(
Response = c(
rnorm(48, mean = 15000, sd = 500)
, rnorm(48, mean = 5000, sd = 500)
, rnorm(48, mean = 1000, sd = 500)
)
, Rep = as.factor(rep(1:3, each = 48))
, Variety = gl(n = 4, k = 4, length = 144, labels = letters[1:4])
, Env = gl(n = 3, k = 16, length = 144, labels = letters[1:3])
)
# Create an instance of the class
gvc1 <- gvc$new(
.data = df1
, .y = Response
, .rep = Rep
, .gen = Variety
, .env = Env
)
# Calculate genetic variance (gvar)
gvc1$calculate_gvar()
# Calculate phenotypic variance (pvar)
gvc1$calculate_pvar()
# Calculate heritability (h2)
gvc1$calculate_herit()
Genotypic Variance Components
Description
Functionalities to compute model based genetic components i.e genotypic, phenotypic variances and heritability for given traits of different genotypes from replicated data using methodology explained by Burton, G. W. & Devane, E. H. (1953) (<doi:10.2134/agronj1953.00021962004500100005x>) and Allard, R.W. (2010, ISBN:8126524154).
Author(s)
Sami Ullah (samiullahuos@gmail.com)
Muhammad Yaseen (myaseen208@gmail.com)
References
R.K. Singh and B.D.Chaudhary Biometrical Methods in Quantitative Genetic Analysis. Kalyani Publishers, New Delhi
Williams, E.R., Matheson, A.C. and Harwood, C.E. (2002).Experimental Design and Analysis for Tree Improvement. CSIRO Publishing.