rankFeatures-SummarizedExperiment-method: Rank the Features in a 'SummarizedExperiment' Object
In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description Usage Arguments Value Examples

Rank the Features in a SummarizedExperiment Object

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

`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.

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.