geneSetSummaryByGenes {sparrow} | R Documentation

## Summarize geneset:feature relationships for specified set of features

### Description

This function creates a geneset by feature table with geneset membership information for the `features` specified by the user. Only the gene sets that have any of the `features` are included in the table returned.

### Usage

    geneSetSummaryByGenes(
      x,
      features,
      with.features = TRUE,
      feature.rename = NULL,
      ...,
      as.dt = FALSE
    )

    ## S4 method for signature 'GeneSetDb'
    geneSetSummaryByGenes(
      x,
      features,
      with.features = TRUE,
      feature.rename = NULL,
      ...,
      as.dt = FALSE
    )

    ## S4 method for signature 'SparrowResult'
    geneSetSummaryByGenes(
      x,
      features,
      with.features = TRUE,
      feature.rename = NULL,
      method = NULL,
      max.p = 0.3,
      p.col = c("padj", "padj.by.collection", "pval"),
      ...,
      as.dt = FALSE
    )

### Arguments

`x` | `GeneSetDb` or `SparrowResult`
`features` | a character vector of featureIds
`with.features` | Include columns for `features`? If `x` is is a `GeneSetDb`, these columns are `TRUE`/`FALSE`. If `x` is a `SparrowResult` object, the values are the logFC of the feature if present in the gene set, otherwise its `NA`.
`feature.rename` | if `NULL`, the feature columns are prefixed with `featureId_`, if `FALSE`, no renaming is done. If `x` is a `SparrowResult`, then this can be the column name found in `logFC(x)`, in which case the value for the feature from the given column name would be used (setting this to `"symbol"`) would be a common thing to do, for instance.
`...` | pass through arguments
`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`
`method` | The GSEA method to pull statistics from
`max.p` | the maximum p-value from the analysis `method` to allow for the geneSets included in the returned table
`p.col` | which p-value column to select from: `'padj'`, `'padj.by.collection'`, or `'pval'`

### Value

a data.frame of geneset <-> feature incidence/feature matrix.

### Methods (by class)

- `SparrowResult`: get geneset:feature incidence table from a SparrowResult, optionally filtered by statistical significance from a given gsea `method`

### Examples

    vm <- exampleExpressionSet(do.voom=TRUE)
    gdb <- conform(exampleGeneSetDb(), vm)
    mg <- seas(vm, gdb, design = vm$design, contrast = 'tumor')
    features <- c("55839", "8522", "29087")
    gsm.hit <- geneSetSummaryByGenes(gdb, features)
    gsm.fid <- geneSetSummaryByGenes(mg, features, feature.rename=NULL)
    gsm.sym <- geneSetSummaryByGenes(mg, features, feature.rename='symbol')

[Package sparrow version 1.0.3 Index]