boxplotPromoters: Visualizes promoter activity and gene expression with...

In GoekeLab/proActiv: Estimate Promoter Activity from RNA-Seq data

Description

Visualizes promoter activity and gene expression with boxplots

Usage

boxplotPromoters(
  result,
  geneId,
  geneName = NULL,
  filterInternal = TRUE,
  col = NULL
)

Arguments

result	A SummarizedExperiment object return by proActiv, with assays giving promoter counts and activity with gene expression stored as metadata. rowData contains promoter metadata and absolute promoter activity summarized across conditions. Condition must be provided.
geneId	A character vector. A single gene id. This identifier must correspond to the identifier in the promoter annotation.
geneName	A character vector. Common gene name to be displayed on plot. Optional. Defaults to NULL.
filterInternal	A boolean. Determines if internal promoters should be removed from the plot. Defaults to TRUE.
col	A character vector of colours to be used for plotting.

Value

A list of length 3. Each entry is a plot corresponding to absolute promoter activity, relative promoter activity and gene expression.

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)
plots <- boxplotPromoters(result, "ENSG00000076864.19")

GoekeLab/proActiv documentation built on Jan. 30, 2022, 3:52 a.m.