R: A list of most parameters.

all {propr} | R Documentation

## A list of most parameters.

### Description

A list of most parameters.

### Arguments

`counts` | 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.
`metric` | A character string. The proportionality metric to calculate. Choose from "rho", "phi", or "phs".
`ivar` | 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.
`select` | Optional. Use this to subset the final proportionality matrix without altering the result. Use this argument to rearrange feature order.
`symmetrize` | A logical. If `TRUE`, forces symmetry by reflecting the "lower left triangle".
`alpha` | A double. See vignette for details. Leave missing to skip Box-Cox transformation.
`p` | An integer. The number of permutation cycles.
`...` | Arguments passed to the wrapped method.
`object, x, rho, propr, propd` | A `propr` or `propd` object.
`subset` | Subsets via `object@counts[subset, ]`. Use this argument to rearrange subject order. For backwards compatibility.
`i` | Operation used for the subset indexing. Select from "==", "=", ">", ">=", "<", "<=", "!=", or "all". For backwards compatibility.
`j` | Provide a numeric value to which to compare the proportionality measures in the `@matrix` slot. For backwards compatibility.
`tiny` | A logical scalar. Toggles whether to pass the indexed result through `simplify`. For backwards compatibility.
`group` | A character vector. Group or sub-group memberships, ordered according to the row names in `counts`.
`weighted` | A boolean. Toggles whether to calculate theta using `limma::voom` weights.
`cutoff` | 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.
`what` | A character string. The theta type to set active.
`moderated` | For `updateF`, a boolean. Toggles whether to calculate a moderated F-statistic.
`y` | Missing. Ignore. Leftover from the generic method definition.
`prompt` | A logical scalar. Set to `FALSE` to disable the courtesy prompt when working with big data.
`plotly` | A logical scalar. Set to `TRUE` to produce a dynamic plot using the `plotly` package.
`k` | 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.
`col1, col2` | A character vector. Specifies which nodes to color `red` or `blue`, respectively.
`d3` | A boolean. Use `rgl` to plot 3D network.
`include` | 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`.
`or` | A boolean. If `FALSE`, `include` subsets by `Partner %in% subset & Pair %in% subset`.
`clean` | A boolean. Toggles whether to remove pairs with "Bridged" or "Missing" PALs. Used by `geyser`, `bowtie`, and `gemini`.
`plotSkip` | A boolean. Toggles whether to build the network graph without plotting it. Used by `pals`.

[Package propr version 4.1.6 Index]