what is the wrong in this command
Q; 2) Run a genome wide association analysis for the trait using Plink?
system("plink_mac/plink --linear --trait/pheno.txt --mpheno 1 --ci 0.95 --adjust --out results_2049669")
gwasresults <- read.table("results_2049669.assoc.linear", header=T)
system in R just invokes the OS command specified by command.
A good first step to diagnosing this issue is to check to ensure that the filename and path are valid. Also note that R with RStudio offer a few options to load files into your environment.
If you internet-search terms like "load .bed file with R", you'll find a number of packages with functions that help you load and work with .bed formatted files.
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