create_pa_rse: Create a RangedSummarizedExperiment from recount3

In eddieimada/REPAC: Differential Alternative Polyadenylation Analysis From Compositions

Create a RangedSummarizedExperiment from recount3

Description

'create_pa_rse creates a RangedSummarizedExperiment object by extracting expression information from recount3 bigWig files from annotated polyA sites provided through a GRanges object. It will also pull relevant metadata for the project through recount3.

Usage

create_pa_rse(
  organism = c("human", "mouse"),
  project = NULL,
  annotation = NULL,
  sample_id = NULL,
  prefix = tempdir()
)

Arguments

organism	A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".
project	A character(1) with the ID for a given study. See available_projects from the recount3 package.
annotation	A GenomicRanges object with the coordinates of annotated PA-sites. This object must have an elementMetadata column named "gene_name" with gene-level IDs.
sample_id	A character vector with the ID(s) for a given sample inside the study. See available_samples from the recount3 package.
prefix	A character() with the path to which temporary files should be written.

Value

A RangedSummarizedExperiment-class object.

Author(s)

Eddie Imada

Examples

## Explore available projects in recount3
human_projects <- recount3::available_projects()

## Find the project you are interested in and obtain PA expression
data(mm10_pa)
create_pa_rse(organism = "mouse", project="SRP048707", annotation=mm10_pa)

eddieimada/REPAC documentation built on Aug. 20, 2023, 7:22 a.m.