Perform Significance Analysis of Function and Expression
KO_safe(
reporter_res,
verbose = TRUE,
perm = 1000,
C.matrix = NULL,
p.adjust.method = "BH",
...
)
The input reporter result.
If TRUE, print verbose messages. Default is TRUE.
The number of permutations. Default is 1000.
The contrast matrix. Default is NULL, and it will be generated from the module list.
Method for p-value adjustment. Default is "BH".
Additional parameters to be passed to safe
function.
A data frame containing SAFE results for KO enrichment.
# \donttest{
## use `safe` from the `safe` package.
if (requireNamespace("safe")) {
data("reporter_score_res")
safe_res <- KO_safe(reporter_score_res,
verbose = TRUE,
perm = 200, p.adjust.method = "none"
)
}
#> Loading required namespace: safe
# }