resultNames {sparrow} | R Documentation

## Interrogate the results of a sparrow::seas analysis stored in a SparrowResult

### Description

The `resultNames`, `result`, and `results` functions enable you to explore the results of the analysis run with `seas()`.

The results that are stored within a `SparrowResult` object have a more or less 1:1 mapping with the values passed as `methods`, parameter of the `seas()` call.

Generates a table to indicate the number of genesets per collection that pass a given FDR. The table provides separate groups of rows for each of the `methods` run in the `seas()` call that generated that generated `x`.

### Usage

    resultNames(x)

    result(x, ...)

    ## S3 method for class 'SparrowResult'
    result(
      x,
      name = NULL,
      stats.only = FALSE,
      rank.by = c("pval", "t", "logFC"),
      add.suffix = FALSE,
      as.dt = FALSE,
      ...
    )

    results(
      x,
      names = resultNames(x),
      stats.only = TRUE,
      rank.by = c("pval", "logFC", "t"),
      add.suffix = length(names) > 1L,
      as.dt = FALSE
    )

    tabulateResults(
      x,
      names = resultNames(x),
      max.p = 0.2,
      p.col = c("padj", "padj.by.collection", "pval"),
      as.dt = FALSE
    )

### Arguments

`x` | A `SparrowResult()` object.
`...` | pass through arguments
`name` | the names of the results desired
`stats.only` | logical, set to `FALSE` if you want to return all (column-wise) data for each result. By default only the pvalues, adjusted pvalues, and rank are returned.
`rank.by` | the statistic to use to append a `rank` column for the geneset result. By default we rank by pvalue calculated by the GSEA method. You can rank the results based on the trimmed mean of the logFC's calculated for all of the features in the geneset (`"logFC"`), or the trimmed t-statistics of the these features (`"t"`).
`add.suffix` | If `TRUE`, adds `.name` as a suffix to the columns of the `method`-specific statistics returned, ie. the `pval` column from the `"camera"` result will be turned to `pval.camera`.
`as.dt` | If `FALSE` (default), the data.frame like thing that this funciton returns will be set to a data.frame. Set this to `TRUE` to keep this object as a `data.table`
`names` | the names of the GSEA methods to be reported. By default, this function will display results for all methods.
`max.p` | The maximum padj value to consider a result significant
`p.col` | use padj or padj.by.collection?

### Details

The product of an indivdual GSEA is consumed by the corresponding `do.<METHOD>` function and converted into a data.table of results that is internally stored.

Use the `resultNames()` function to identify which results are available for interrogation. The `result()` function returns the statistics of one individual result, and the `results()` function combines the results from the specified methods into an arbitrarily wide data.table with `method`-suffixed column names.

Use the `tabulateResults()` function to create a summary table that tallies the number of significant genesets per collection, per method at the specified FDR thresholds.

### Value

a data.table with the results from the requested method.

a data.table that summarizes the significant results per method per collection for the GSEA that was run

### Examples

    res <- exampleSparrowResult()
    resultNames(res)
    head(result(res, "camera"))
    head(results(res))

[Package sparrow version 1.0.3 Index]