rankFeatures,SummarizedExperiment-method {PDATK} | R Documentation

## Rank the Features in a `SummarizedExperiment` Object

### Description

Rank the Features in a `SummarizedExperiment` Object

### Usage

    ## S4 method for signature 'SummarizedExperiment'
    rankFeatures(
      object,
      FUN = "rowMads",
      RANK_FUN = "dense_rank",
      ...,
      descending = TRUE,
      assay = 1
    )

### Arguments

`object` | A `SummarizedExperiment` to rank the features in.
`FUN` | A row-wise summary function, such as `rowVars`, `rowMads`, etc. defaults to `MatrixGenerics::rowMads`.
`RANK_FUN` | A ranking function, such as `rank` or `dense_rank`. Defaults to `dplyr::dense_rank`.
`...` | Fall through arguments to `FUN`, such as `na.rm=TRUE`.
`descending` | Should your rank function be called with `-` before the values from `FUN`. Defaults to `TRUE`.
`assay` | `integer` assay to use for the ranking, as passed to the `SummarizedExperiment::assay` function. Defaults to the first assay.

### Value

The `SummarizedExperiment` with the column `feature_score` and `feature_rank` in the `rowData` slot. Information about which functions where used for each column can be found in the object `mcols` in the `calculated_with` column.

### Examples

    data(sampleICGCmicro)
    rankFeatures(sampleICGCmicro, FUN='rowMads', RANK_FUN='dense_rank')

[Package PDATK version 1.2.0 Index]