R: Find Clusters with High/Low P-values

pvpick {pvclust} | R Documentation

## Find Clusters with High/Low P-values

### Description

find clusters with relatively high/low p-values. `pvrect` and `lines` (S3 method for class `pvclust`) highlight such clusters in existing plot, and `pvpick` returns a list of such clusters.

### Usage

    pvpick(x, alpha=0.95, pv="au", type="geq", max.only=TRUE)

    pvrect(x, alpha=0.95, pv="au", type="geq", max.only=TRUE, border=2, ...)

    ## S3 method for class 'pvclust'
    lines(x, alpha=0.95, pv="au", type="geq", col=2, lwd=2, ...)

### Arguments

`x` | object of class `pvclust`.
`alpha` | threshold value for p-values.
`pv` | character string which specifies the p-value to be used. It should be either of `"au"` or `"bp"`, corresponding to AU p-value or BP value, respectively. See `plot.pvclust` for details.
`type` | one of `"geq"`, `"leq"`, `"gt"` or `"lt"`. If `"geq"` is specified, clusters with p-value greater than or equals the threshold given by `"alpha"` are returned or displayed. Likewise `"leq"` stands for lower than or equals, `"gt"` for greater than and `"lt"` for lower than the threshold value. The default is `"geq"`.
`max.only` | logical. If some of clusters with high/low p-values have inclusion relation, only the largest cluster is returned (or displayed) when `max.only=TRUE`.
`border` | numeric value which specifies the color of borders of rectangles.
`col` | numeric value which specifies the color of lines.
`lwd` | numeric value which specifies the width of lines.
`...` | other graphic parameters to be used.

### Value

`pvpick` returns a list which contains the following values.

`clusters` | a list of character string vectors. Each vector corresponds to the names of objects in each cluster.
`edges` | numeric vector of edge numbers. The i'th element (number) corresponds to the i'th name vector in `clusters`.

### Author(s)

Ryota Suzuki suzuki@ef-prime.com

[Package pvclust version 2.0-0 Index]