statDesign: Statistic of optimal genome
In GOVS-pack/GOVS: Genome optimization via virtual simulation

statDesign

R Documentation

Statistic of optimal genome

Description

Statistic summary for analysis of the contribution of all candidates to optimal genome. The results directly guide the lines selection and population improvement route.

Usage

statDesign(designInfo,which = "max",binsInfo,pheno,trait,output = NULL)

Arguments

`designInfo`	Outputs of `genomeOptimization`, a matrix consists of sample IDs regarding the fragment source among condidates at each bin locus.
`binsInfo`	Data frame, including bins index, start, end, length of bins locus.
`which`	A character, defining which virtual genome used for statistics, default "max".
`pheno`	Phenotypic data frame, the first column describes sample names.
`trait`	The names of interest trait (The trait must be included in 'Pheno' data frame).
`output`	The prefix of output files regarding the summary and statistic infomation via the process of genome optimization.

Value

A data frame regarding statistics results of virtual simulation.

`Lines`	Lines
`Bins(#)`	The number (#) of bins that a line contributed to the simulated genome.
`Bins(%)`	The number of bins that a line contributed accounting for the proportion (%) of simulated genome.
`Fragments(%)`	The total length of genomic fragments that a line contributed accounting for the proportion (%) of simulated genome.
`phenotype`	The phenotypic value of the corresponding lines or their offspring
`phenotypeRank`	The phenotype rank
`Cumulative(%)`	The cumulative percentage of fragments contributing to the simulated genome.

If output is defined, the statistics results will be written to file with suffix "statRes.csv".

Author(s)

Qian Cheng, Shuqin Jiang, Xiangfeng Wang

Examples

## Not run !
## load test data
# Phenotypic data:
data(phe)
# bins data:
data(bins)

# 1.run example for EW trait (write result files to local)
genomeOptimization(pheno = phe,trait = "EW",bins = bins,output = "MZ_test_1404")

# 2.run example for EW trait (get the results of genomeOptimization in R)
GO_res <- genomeOptimization(pheno = phe,trait = "EW",bins = bins,output = NULL)

# 3.Statistics for genome optimization
sta_res <- statDesign(designInfo = GO_Res$overall,binInfo = binsInfo,pheno = phe,
                      trait = "EW")

GOVS-pack/GOVS documentation built on Oct. 9, 2022, 8:29 a.m.