genomeOptimization: Genome optimization function

In GOVS-pack/GOVS: Genome optimization via virtual simulation

Genome optimization function

Description

Virtual genome optimization based IBD(bins) data

Usage

genomeOptimization(pheno,bins,trait,output = NULL)

Arguments

pheno	Phenotypic data frame, the first column describes sample names.
bins	Results of IBD analysis (bins matrix), each row represents a bin fragment as well as each column represents each sample.
trait	The names of interest trait (The trait must be included in 'Pheno' data frame
output	The prefix of output files regarding the scheme of virtual genome.

Value

Genome optimization results

max	Details for "optimal" simulation
med	Details for "moderate" simulation
min	Details for "poor" simulation
overall	Lines' names for genome optimization results of three simulated genome. Used for extractGenome
pvalue	P-value for ANOVA

If output is defined, all above five elements will be written to five files with suffix ".max", ".med",".min", ".merge",".pvalue".

Author(s)

Qian Cheng, Shuqin Jiang, Xiangfeng Wang

See Also

GOVS

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)

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