I am new in eQTL. I am trying to work in Matrix EQTL in R. I have gene expression txt file and SNP.txt file. In SNP.txt , I don't have all rsids.
- May I have to remove those SNPs where no rsid is assigned?
- When I am uploading text file in R then it shows error in file (description = filename, open = rt, blocking = false, raw = false)
Kindly help me to analyze eQTL in R or any other tool .
Apparantly you're trying to import the data from a wrong location. Try the following code
useModel = modelLINEAR
SNP_file_name = paste("/Users/user1/Desktop/Plant_1/eqtl/209_40.txt", sep = "")
expression_file_name = paste( "/Users/user1/Desktop/Plant_1/eqtl/Gene_expression.txt.", sep = "")
#covariates_file_name to character() Error: unexpected symbol in "covariates_file_name to" covariates_file_name = character()
output_file_name = tempfile()
pvOutputThreshold = 1e-2
errorCovariance = numeric()
snps = SlicedData$new()
snps$fileDelimiter = "\t"
snps$fileOmitCharacters = "NA"
snps$fileSkipRows = 1
snps$fileSkipColumns = 1
snps$fileSliceSize = 2000
snps$LoadFile( SNP_file_name )
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