A list of most parameters.
A data.frame or matrix. A "count matrix" with subjects as rows and features as columns. Note that this matrix does not necessarily have to contain counts.
A character string. The proportionality metric to calculate. Choose from "rho", "phi", or "phs".
A numeric scalar. Specifies reference feature(s) for additive log-ratio transformation. The argument will also accept feature name(s) instead of the index position(s). Set to "iqlr" to use inter-quartile log-ratio transformation. Ignore to use centered log-ratio transformation.
Optional. Use this to subset the final proportionality matrix without altering the result. Use this argument to rearrange feature order.
A logical. If TRUE, forces symmetry
by reflecting the "lower left triangle".
A double. See vignette for details. Leave missing to skip Box-Cox transformation.
An integer. The number of permutation cycles.
Arguments passed to the wrapped method.
A propr or propd object.
Subsets via object@counts[subset, ].
Use this argument to rearrange subject order.
For backwards compatibility.
Operation used for the subset indexing. Select from "==", "=", ">", ">=", "<", "<=", "!=", or "all". For backwards compatibility.
Provide a numeric value to which to compare the
proportionality measures in the @matrix slot.
For backwards compatibility.
A logical scalar. Toggles whether to pass the indexed
result through simplify.
For backwards compatibility.
A character vector. Group or sub-group memberships,
ordered according to the row names in counts.
A boolean. Toggles whether to calculate
theta using limma::voom weights.
For updateCutoffs, a numeric vector.
this argument provides the FDR cutoffs to test.
For graph functions, a numeric scalar. This argument
indicates the maximum theta to include in the figure.
For graph functions, a large integer will instead
retrieve the top N pairs as ranked by theta.
A character string. The theta type to set active.
For updateF, a boolean. Toggles
whether to calculate a moderated F-statistic.
An integer. The number of parallel cores to use.
Missing. Ignore. Leftover from the generic method definition.
A logical scalar. Set to FALSE to disable
the courtesy prompt when working with big data.
A logical scalar. Set to TRUE to produce
a dynamic plot using the plotly package.
An integer. For propr methods, the number
of co-clusters (where all pairs receive a specified color
if and only if both members belong to same the cluster).
For propd methods, the maximum number of PALs to index
when calculating pals in the network.
A character vector. Specifies which nodes
to color red or blue, respectively.
A boolean. Use rgl to plot 3D network.
This argument indicates which features by
name should belong to a pair for that pair to get included
in the results. Subset performed by
Partner %in% subset | Pair %in% subset.
A boolean. If FALSE, include subsets
by Partner %in% subset & Pair %in% subset.
A boolean. Toggles whether to remove pairs
with "Bridged" or "Missing" PALs. Used by geyser,
bowtie, and gemini.
A boolean. Toggles whether to build
the network graph without plotting it.
Used by pals.