rankFeatures-SummarizedExperiment-method: Rank the Features in a 'SummarizedExperiment' Object

Description Usage Arguments Value Examples

Description

Rank the Features in a SummarizedExperiment Object

Usage

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## 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

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

bhklab/PDATK documentation built on Dec. 27, 2021, 7:46 a.m.