I would like to analyze rare variants for WGS data using SAIGE-GENE.
Then I ran createSparseGRM.R to perform the "Step 0: Creating a sparse GRM" process, and the code is as below.
option_list <- list(
make_option("--plinkFile", type="character",default="",
help="path to plink file for creating the genetic relationship matrix (GRM)"),
make_option("--nThreads", type="integer", default=16,
help="Number of threads (CPUs) to use"),
make_option("--memoryChunk", type="numeric", default=2,
help="The size (Gb) for each memory chunk. By default, 2"),
make_option("--outputPrefix", type="character", default="~/",
help="path and prefix to the output files [default='~/']"),
make_option("--numRandomMarkerforSparseKin", type="integer", default=2000,
help="number of randomly selected markers to be used to identify related samples for sparse GRM [default=2000]"),
make_option("--relatednessCutoff", type="numeric", default=0.125,
help="The threshold to treat two samples as unrelated if IsSparseKin is TRUE [default=0.125]"),
make_option("--isDiagofKinSetAsOne", type="logical", default=FALSE,
help="Whether to set the diagnal elements in GRM to be 1 [default='FALSE']."),
make_option("--minMAFforGRM", type="numeric", default=0.01,
help="minimum MAF of markers used for GRM")
)
I would like to analyze rare variants for WGS data using SAIGE-GENE. Then I ran createSparseGRM.R to perform the "Step 0: Creating a sparse GRM" process, and the code is as below.
`#!/usr/bin/env Rscript
options(stringsAsFactors=F)
load R libraries
library(SAIGE, lib.loc="/home/wei/install_dir/0.36.5.1")
library(SAIGE) require(optparse) #install.packages("optparse")
print(sessionInfo())
set list of cmd line arguments
option_list <- list( make_option("--plinkFile", type="character",default="", help="path to plink file for creating the genetic relationship matrix (GRM)"), make_option("--nThreads", type="integer", default=16, help="Number of threads (CPUs) to use"), make_option("--memoryChunk", type="numeric", default=2, help="The size (Gb) for each memory chunk. By default, 2"), make_option("--outputPrefix", type="character", default="~/", help="path and prefix to the output files [default='~/']"), make_option("--numRandomMarkerforSparseKin", type="integer", default=2000, help="number of randomly selected markers to be used to identify related samples for sparse GRM [default=2000]"), make_option("--relatednessCutoff", type="numeric", default=0.125, help="The threshold to treat two samples as unrelated if IsSparseKin is TRUE [default=0.125]"), make_option("--isDiagofKinSetAsOne", type="logical", default=FALSE, help="Whether to set the diagnal elements in GRM to be 1 [default='FALSE']."), make_option("--minMAFforGRM", type="numeric", default=0.01, help="minimum MAF of markers used for GRM") )
list of options
parser <- OptionParser(usage="%prog [options]", option_list=option_list) args <- parse_args(parser, positional_arguments = 0) opt <- args$options print(opt)
set.seed(1)
createSparseGRM(plinkFile = opt$plinkFile, outputPrefix=opt$outputPrefix, numRandomMarkerforSparseKin = opt$numRandomMarkerforSparseKin, relatednessCutoff = opt$relatednessCutoff, memoryChunk = opt$memoryChunk, isDiagofKinSetAsOne = opt$isDiagofKinSetAsOne, nThreads = opt$nThreads, minMAFforGRM = opt$minMAFforGRM)`
Rscript createSparseGRM.R \ --plinkFile=/input_path/WGS_plink_file \ --nThreads=4 \ --outputPrefix=./output/sparseGRM \ --numRandomMarkerforSparseKin=2000 \ --relatednessCutoff=0.125But I got an error code Error in createSparseGRM(plinkFile = opt$plinkFile, outputPrefix = opt$outputPrefix, : unused argument (plinkFile = opt$plinkFile) Execution halted
How can I solve this problem?