run_GenSel4: 'Run GenSel on slurm-based HPC'

In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description

GenSel4R

Usage

run_GenSel4(inputdf, cv = FALSE, bayesType = "BayesC",
  inpdir = "largedata/", cmdno = 1,
  shid = "slurm-script/run_gensel_array.sh", remove = TRUE,
  email = NULL, runinfo = c(FALSE, "batch", "30", 3, "8:00:00"))

Arguments

inputdf	An input data.frame for this function, including all the necessary pheno, geno file pathes, and other parameters. [data.frame, see exaples]
cv	Cross-validation experiment [TRUE/FALSE, default=FALSE]. If TRUE, inputdf must contain 'trainpheno' and 'testpheno'; if FALSE, only need 'pheno'.
bayesType	Analysis types for Bayes Methods. [chr, default=BayesC; BayesA, BayesB, BayesC, BayesCPi, RBR]
inpdir	Dir for the GS .inp file. [chr, default="largedata/"].
cmdno	Number of commands per CPU, i.e. number of rows per inputdf. [num, default=1].
shid	The shell ID for this job. [chr, default is "slurm-script/run_gensel_array.sh"].
remove	Whether to remove the intermediate GS files or not. [TRUE/FALSE, default is TRUE].
email	Your email address that farm will email to once the jobs were done/failed. [chr, default is NULL]
runinfo	Parameters specify the array job partition information. A vector of c(FALSE, "batch", "30G", 1, "8:00:00"): 1) run or not, default=FALSE 2) -p partition name, default=batch, 3) –ntasks=3, 4) –mem=30G, and 5) –time=8:00:00.

Value

return a batch of shell scripts.

Examples

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, cv=FALSE, inpdir="slurm-script/", cmdno=1,
            shid = "slurm-script/run_gensel_array.sh", remove=TRUE,
            email=NULL, runinfo = c(FALSE, "batch", 3, "30", "8:00:00") )

yangjl/huskeR documentation built on Sept. 2, 2021, 5:38 a.m.