R: Build 'propd' Results Table

shale {propr} | R Documentation

## Build `propd` Results Table

### Description

Builds a table of within-group and total log-ratio variances, log-ratio means, and PALs (see: `pals`). If the argument `k` is provided, the table will label at most `k` top PALs. Just as each node gets assigned a PAL, `shale` aims to assign each edge a PAL. Edges that have a top PAL as one and only one of their nodes get assigned that PAL. Edges that have top PALs as both of their nodes get assigned "Bridged". Edges without a top PAL as one of their nodes will get assigned a PAL if either (a) both nodes have the same neighbor PAL or (b) one node has a "Missing" neighbor PAL. The `cutoff` argument guides the maximum value of theta above which to exclude the pair. A large integer `cutoff` will instead retrieve the top N pairs as ranked by theta.

### Usage

    shale(object, cutoff = 1000, k, prompt = TRUE, clean = FALSE)

### Arguments

`object` | A `propr` or `propd` object.
`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.
`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.
`prompt` | A logical scalar. Set to `FALSE` to disable the courtesy prompt when working with big data.
`clean` | A boolean. Toggles whether to remove pairs with "Bridged" or "Missing" PALs. Used by `geyser`, `bowtie`, and `gemini`.

[Package propr version 4.2.6 Index]