diff --git a/man/propr.Rd b/man/propr.Rd index ff2a400..f76f687 100755 --- a/man/propr.Rd +++ b/man/propr.Rd @@ -17,8 +17,7 @@ propr( select = NA, symmetrize = FALSE, alpha = NA, - p = 0, - ... + p = 0 ) } \arguments{ @@ -62,9 +61,6 @@ will symmetrize the matrix; otherwise, it will return the original matrix.} \item{p}{The number of permutations to perform for calculating the false discovery rate (FDR). The default is 0.} - -\item{...}{Additional arguments passed to \code{corpcor::pcor.shrink}, -if "pcor.shrink" metric is selected.} } \value{ A propr object containing the Propr matrix, associated log-ratio diff --git a/man/updateCutoffs.Rd b/man/updateCutoffs.Rd index f43ba35..775d05e 100644 --- a/man/updateCutoffs.Rd +++ b/man/updateCutoffs.Rd @@ -9,23 +9,23 @@ updateCutoffs( object, number_of_cutoffs = 100, - custom_cutoffs = NULL, - tails = NULL, + custom_cutoffs = NA, + tails = NA, ncores = 1 ) updateCutoffs.propr( object, number_of_cutoffs = 100, - custom_cutoffs = NULL, - tails = NULL, + custom_cutoffs = NA, + tails = NA, ncores = 1 ) updateCutoffs.propd( object, number_of_cutoffs = 100, - custom_cutoffs = NULL, + custom_cutoffs = NA, ncores = 1 ) } @@ -39,8 +39,8 @@ cutoffs will be evenly spaced across the data.} \item{custom_cutoffs}{A numeric vector. When provided, this vector is used as the set of cutoffs to test, and 'number_of_cutoffs' is ignored.} -\item{tails}{NULL or 'right' or 'both'. 'right' is for one-sided on the right. 'both' for -symmetric two-sided test. If NULL, use default value according to the property +\item{tails}{NA or 'right' or 'both'. 'right' is for one-sided on the right. 'both' for +symmetric two-sided test. If NA, use default value according to the property `has_meaningful_negative_values`. This is only relevant for \code{propr} objects, as \code{propd} objects are always one-sided and only have positive values.}