p.matrix {sparrow} | R Documentation

## Assembles a matrix of nominal or adjusted pvalues from a sparrow::seas result

### Description

You might want a matrix of pvalues (or FDRs) for the gene sets across all GSEA methods you tried. I think I did, once, so here it is.

### Usage

    p.matrix(
      x,
      names = resultNames(x),
      pcol = c("padj", "padj.by.collection", "pval")
    )

### Arguments

`x` | A `SparrowResult()` object.
`names` | the entries from `resultNames(x)` that you want to include in the matrix. By default we take all of them.
`pcol` | The name of the column in `logFC(x)` where the type of pvalues are that we are collection. Pick on of `"padj"`, `"padj.by.collection"`, or `"pval"`

### Value

A matrix of the desired pvalues for all genesets

### Examples

    mg <- exampleSparrowResult()
    pm <- p.matrix(mg)

[Package sparrow version 1.0.3 Index]