run_gerpIBD: 'Run gerpIBD on farm'

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

Description

gerpIBD: compute sum of GERP score in a given IBD region across genotypes.

Usage

run_gerpIBD(inputdf, email = NULL, runinfo = c(FALSE, "bigmemh", 1))

Arguments

inputdf	An input data.frame. Type "gerpIBD -h" to understand the meaning of the input parameters.
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(trait=rep(traits, each=44),
   mode=rep(rep(c("add", "dom", "k", "k5"), each=11), times=7 ),
   nperm=rep(0:10, times=28),
   d="largedata/IBD/allsnps_11m_IBD.bed",
   s="largedata/SNP/allsnps_11m.dsf5",
   g="largedata/SNP/geno_b0_cs/gerpv2_b0_cs0.csv",
   f="largedata/snpeff/perse/asi_k.txt",
   out="res")

run_gerpIBD(inputdf[1:10,], email=NULL, runinfo = c(FALSE, "bigmemh", 1) )

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