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maturing The GWAS function writes all results, both valid and invalid, to a log file. This function uses heuristics to try to classify rows as suspicious or unsuspicious.
isSuspicious(result, pars = attr(result, "focus"))
output from loadResults
names of the parameters available in result
a vector of logicals for each row of result
indicating suspicion (if TRUE)
OpenMx reports exceptions in the ‘catch1’
column. Any error message in the ‘catch1’ column is
suspicious. Any optimizer status code besides ‘OK’ is
suspicious. It is suspicious if the focal parameter or its
standard error is NA
. If ‘signAdj’ was requested
and it is NA
then suspicion is also aroused.
Other reporting:
loadResults()
,
plot.gwsemResult()
,
signifGxE()
,
signif()
# NOT RUN {
tdir <- tempdir()
dir <- system.file("extdata", package = "gwsem")
pheno <- data.frame(anxiety=rnorm(500))
m1 <- buildItem(pheno, 'anxiety')
GWAS(m1, file.path(dir,"example.bgen"),
file.path(tdir,"out.log"))
r1 <- loadResults(file.path(tdir,"out.log"), "snp_to_anxiety")
r1[isSuspicious(r1, "snp_to_anxiety"),]
# }
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