FaST-LMM
What is FaST-LMM?
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-pheno : Denotes the name of the phenotype file (including extension)-covar : Denotes the name of the covariate file (including file extension)
-out : The name of your final output file, which is placed into the same directory as your program and data unless otherwise specified
- -fileSim: The name of the PLINK set used for computing the genetic similarity matrix and its decomposition (will be the same as the fileset used, hence, file extension not necessary)
Additional options
-verboseOutput : use this flag to show more complex and detailed output; does not require a file to be named
- -fileSimcovar : The Denotes the name of the PLINK set used for computing the genetic similarity matrix and its decompositioncovariate file (including file extension)
-pValuePrintThreshold : Restricts the output file to only include SNPs with a p-value less than or equal to the specified threshold
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| Code Block |
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fastlmmc -verboseOutput -file <filename> -fileSim <filename> -pheno <filename.phe.txt>txt or filename.pehno> -covar <filename.covar.txt> -out MyResults.csv -pValuePrintThreshold 0.05 |
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