GOVS: Genome optimization via virtual simulation

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

Genome optimization via virtual simulation

Description

One-stop function for a complete progress of genome optimization.

Usage

 GOVS(hmp,ID = NULL,pheno,trait,bins,binsInfo,which = "max",
      output = NULL,module = "DES",designInfo,extractContent = "Genotype")

Arguments

hmp	The genetic data in hapmap format.
ID	A character array regarding sample IDs for "hmp", if NULL, the "hmp" data must involve header.
pheno	Phenotypic data frame, the first column describes sample IDs.
trait	The names of interest trait (The trait must be included in "Pheno" data frame).
bins	Results of IBD analysis (bins matrix), each row represents a bin fragment as well as each column represents each sample.
binsInfo	Data frame, including bins index, start, end, length of bins locus.
which	A character, defining which virtual genome used for statistics, default "max".
output	The prefix of output files.
module	Character represents the module combination for analysis, default "DES", "D" for genome optimization module, "E" for extraction & assembly module. "S" for statistic module. "D","E","S","DE","DES" and "ES" are alternative for different module combinations. Note that different combination need different essential inputs.
designInfo	Data frame, the results of genome optimization module, it's necessary for "ES" and "S" module.
extractContent	Character, the content of virtual genome, "Bin" for bin source well "Genotype" for genetic data, default "Genotype".

Value

A list regarding defined module.
If output is defined, all files will be written to file with prefix of "output".

Details see:
genomeOptimization
extractGenome
statDesign

Author(s)

Qian Cheng, Shuqin Jiang, Xiangfeng Wang

See Also

genomeOptimization
extractGenome
statDesign

Examples

## Not run !
## load test data
# Phenotypic data:
data(phe)
# genomic data:
data(MZ)
# bins data:
data(bins)
# bins information:
data(binsInfo)
# example for one-stop solution for GOVS
GOVS_res <- GOVS(MZ,pheno = phe,trait = "EW",which = "max",bins = bins,
                 binsInfo = binsInfo,module = "DES")

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