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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$minMAFforGRM)`
Rscript createSparseGRM.R \ --plinkFile=/input_path/WGS_plink_file \ --nThreads=4 \ --outputPrefix=./output/sparseGRM \ --numRandomMarkerforSparseKin=2000 \ --relatednessCutoff=0.125
But I got an error code
Error in createSparseGRM(plinkFile = opt$plinkFile, outputPrefix = opt$outputPrefix, :
unused argument (plinkFile = opt$plinkFile)
Execution halted
How can I solve this problem?
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