# NOT RUN {
## An example using the "regionGWAS" mode
fastcmh <- CASMAP(mode="regionGWAS") # initialise object
datafile <- getExampleDataFilename() # file name of example data
labelsfile <- getExampleLabelsFilename() # file name of example labels
covfile <- getExampleCovariatesFilename() # file name of example covariates
# read the data, labels and covariate files
fastcmh$readFiles(genotype_file=getExampleDataFilename(),
phenotype_file=getExampleLabelsFilename(),
covariate_file=getExampleCovariatesFilename() )
# execute the algorithm (this may take some time)
fastcmh$execute()
#get the summary results
summary_results <- fastcmh$getSummary()
#get the significant regions
sig_regions <- fastcmh$getSignificantRegions()
#get the clustered representatives for the significant regions
sig_cluster_rep <- fastcmh$getSignificantClusterRepresentatives()
## Another example of regionGWAS
fais <- CASMAP(mode="regionGWAS") # initialise object
# read the data and labels, but no covariates
fastcmh$readFiles(genotype_file=getExampleDataFilename(),
phenotype_file=getExampleLabelsFilename())
## Another example, doing higher order epistasis search
facs <- CASMAP(mode="higherOrderEpistasis") # initialise object
# }
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