getAlternativePromoters {proActiv} | R Documentation

## Identifies alternative promoters.

### Description

Identifies alternative promoters.

### Usage

    getAlternativePromoters(
      result,
      referenceCondition,
      minAbs = 0.25,
      minRel = 0.05,
      maxPval = 0.05,
      promoterFC = 2,
      geneFC = 1.5
    )

### Arguments

`result` | A SummarizedExperiment object with assays giving promoter counts, activity and gene expression (output from proActiv). rowData contains promoter metadata and absolute promoter activity summarized across conditions. Condition must be provided.
`referenceCondition` | A character vector. The reference condition to be compared. Samples corresponding to all other conditions will be compared to this samples in this current condition.
`minAbs` | A numeric value. Minimum value for promoter to be active in absolute terms. Defaults to 0.25.
`minRel` | A numeric value. Minimum value for promoter to be active in relative terms. Defaults to 0.05.
`maxPval` | A numeric value. Adjusted p-value threshold for detecting alternative promoters. Defaults to 0.05.
`promoterFC` | A numeric value. Minimum fold change for a promoter in the current condition compared to all other conditions. Promoters must have at least this magnitude of fold change for alternative usage.
`geneFC` | A numeric value. Maximum fold change for gene expression. To identify alternative promoter usage independent of changes in gene expression, limit the gene expression fold change.

### Value

A list of length 2. Each entry is a dataframe summarizing up-regulated and down-regulated promoters and their corresponding genes, if any.

### Examples

    files <- list.files(system.file('extdata/vignette/junctions',
                           package = 'proActiv'),
                           full.names = TRUE, pattern = 'replicate5')
    promoterAnnotation <- promoterAnnotation.gencode.v34.subset
    result <- proActiv(files = files,
                           promoterAnnotation  = promoterAnnotation,
                           condition = rep(c('A549', 'HepG2'), each=1),
                           fileLabels = NULL,
                           ncores = 1)
    alternativePromoters <- getAlternativePromoters(result, "A549")

[Package proActiv version 1.4.0 Index]