getAlternativePromoters: Identifies alternative promoters.

Description Usage Arguments Value Examples

View source: R/identify-alternative-promoters.R

Description

Identifies alternative promoters.

Usage

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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

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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")

GoekeLab/proActiv documentation built on June 26, 2021, 6:39 a.m.