run_GenSel4: 'Run GenSel on farm'

In yangjl/farmeR: Generate pipelines for maize Genomic and Genetic analysis

Description

GenSel4R

Usage

run_GenSel4(inputdf, cv = FALSE, inpdir = "largedata/", cmdno = 1,
  shid = "slurm-script/run_gensel_array.sh", email = NULL,
  runinfo = c(FALSE, "bigmemh", 1))

Arguments

inputdf	An input data.frame.
cv	Cross-validation experiment [TRUE/FALSE, default=FALSE]. If TRUE, inputdf must contain 'trainpheno' and 'testpheno'; if FALSE, only need 'pheno'.
cmdno	Number of commands per CPU, i.e. number of rows per inputdf.
email	Your email address that farm will email to once the jobs were done/failed.
runinfo	Parameters specify the array job partition information. A vector of c(FALSE, "bigmemh", "1"): 1) run or not, default=FALSE 2) -p partition name, default=bigmemh and 3) –cpus, default=1. It will pass to set_array_job.

Details

see more detail about gerpIBD https://github.com/yangjl/zmSNPtools

Value

return a batch of shell scripts.

Examples

traits <- tolower(c("ASI", "DTP", "DTS", "EHT", "GY", "PHT", "TW"))
inputdf <- data.frame(pi=0.995,
   geno="/Users/yangjl/Documents/GWAS2_KRN/SNP/merged/geno_chr.newbin",
   trainpheno="/Users/yangjl/Documents/Heterosis_GWAS/pheno2011/reports/cd_GenSel_fullset.txt",
   testpheno="/Users/yangjl/Documents/Heterosis_GWAS/pheno2011/reports/cd_GenSel_fullset.txt",
   chainLength=1000, burnin=100, varGenotypic=1.4, varResidual=2,
   out="test_out")

run_GenSel4(inputdf, inpdir="slurm-script", email=NULL, runinfo = c(FALSE, "bigmemh", 1) )

yangjl/farmeR documentation built on May 4, 2019, 2:28 p.m.