geneSetsStats {sparrow} | R Documentation

## Summarizes useful statistics per gene set from a SparrowResult

### Description

This function calculates the number of genes that move up/down for the given contrasts, as well as mean and trimmed mean of the logFC and t-statistics. Note that the statistics calculated and returned here are purely a function of the statistics generated at the gene-level stage of the analysis.

### Usage

    geneSetsStats(
      x,
      feature.min.logFC = 1,
      feature.max.padj = 0.1,
      trim = 0.1,
      reannotate.significance = FALSE,
      as.dt = FALSE
    )

### Arguments

`x` | A `SparrowResult` object
`feature.min.logFC` | used with `feature.max.padj` to identify the individual features that are to be considered differentially expressed.
`feature.max.padj` | used with `feature.min.logFC` to identify the individual features that are to be considered differentially expressed.
`trim` | The amount to trim when calculated trimmed `t` and `logFC` statistics for each geneset.
`reannotate.significance` | this is internally by the package, and should left as `FALSE` when used by the user.
`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`

### Value

A data.table with statistics at the gene set level across the prescribed contrast run on `x`. These statistics are independent of any particular GSEA method, but rather summarize aggregate shifts of the gene sets individual features. The columns included in the output are summarized below:

- `n.sig`: The number of individual features whose `abs(logFC)` and padj thersholds satisfy the criteria of the `feature.min.logFC` and `feature.max.padj` parameters of the original `seas()` call

- `n.neutral`: The number of individual features whose abs(logFC) and padj thersholds do not satisfy the `feature.*` criteria named above.

- `n.up, n.down`: The number of individual features with `logFC > 0` or `logFC < 0`, respectively, irrespective of the `feature.*` thresholds referenced above.

- `n.sig.up, n.sig.down`: The number of individual features that pass the `feature.*` thresholds and have logFC > 0 or logFC < 0, respectively.

- `mean.logFC, mean.logFC.trim`: The mean (or trimmed mean) of the individual logFC estimates for the features in the gene set. The amount of trim is specified in the `trim` parameter of the `seas()` call.

- `mean.t, mean.t.trim`: The mean (or trimmed mean) of the individual t-statistics for the features in the gene sets. These are `NA` if the input expression object was a `DGEList`.

### Examples

    vm <- exampleExpressionSet(do.voom=TRUE)
    gdb <- exampleGeneSetDb()
    mg <- seas(vm, gdb, design = vm$design, contrast = 'tumor')
    head(geneSetsStats(mg))

[Package sparrow version 1.0.3 Index]