preprocess {idr2d} | R Documentation |
This method removes invalid values, establishes the correct ranking, and breaks ties prior to IDR analysis.
Inf
and -Inf
are replaced by max(x) * max_factor
and min(x) / max_factor
, respectively.
NA
values in x
are replaced by mean(x)
.
All values in x
are transformed using the transformation specified
in value_transformation
.
Lastly, a small amount of noise is added to x
to break ties. The
magnitude of the noise is controlled by jitter_factor
.
preprocess( x, value_transformation = c("identity", "additive_inverse", "multiplicative_inverse", "log", "log_additive_inverse"), max_factor = 1.5, jitter_factor = 1e-04 )
x |
numeric vector of values | ||||||||||
value_transformation |
the values in
either | ||||||||||
max_factor |
numeric; controls the replacement values for | ||||||||||
jitter_factor |
numeric; controls the magnitude of the noise that
is added to |
numeric vector; transformed and stripped values of x
, ready
for IDR analysis
rep1_df <- idr2d:::chiapet$rep1_df rep1_df$fdr <- preprocess(rep1_df$fdr, "log_additive_inverse")