expressed_regions: Identify expressed regions from the mean coverage for a given...

In leekgroup/recount: Explore and download data from the recount project

Identify expressed regions from the mean coverage for a given SRA project

Description

This function uses the pre-computed mean coverage for a given SRA project to identify the expressed regions (ERs) for a given chromosome. It returns a GRanges-class object with the expressed regions as defined by findRegions.

Usage

expressed_regions(
  project,
  chr,
  cutoff,
  outdir = NULL,
  maxClusterGap = 300L,
  chrlen = NULL,
  verbose = TRUE,
  ...
)

Arguments

project	A character vector with one SRA study id.
chr	A character vector with the name of the chromosome.
cutoff	The base-pair level cutoff to use.
outdir	The destination directory for the downloaded file(s) that were previously downloaded with download_study. If the files are missing, but outdir is specified, they will get downloaded first. By default outdir is set to NULL which will use the data from the web. We only recommend downloading the full data if you will use it several times.
maxClusterGap	This determines the maximum gap between candidate ERs.
chrlen	The chromosome length in base pairs. If it's NULL, the chromosome length is extracted from the Rail-RNA runs GitHub repository. Alternatively check the SciServer section on the vignette to see how to access all the recount data via a R Jupyter Notebook.
verbose	If TRUE basic status updates will be printed along the way.
...	Additional arguments passed to download_study when outdir is specified but the required files are missing.

Value

A GRanges-class object as created by findRegions.

Author(s)

Leonardo Collado-Torres

See Also

download_study, findRegions, railMatrix

Examples

## Define expressed regions for study SRP002001, chrY

## Workaround for https://github.com/lawremi/rtracklayer/issues/83
download_study("SRP002001", type = "mean")

regions <- expressed_regions("SRP002001", "chrY",
    cutoff = 5L,
    maxClusterGap = 3000L,
    outdir = "SRP002001"
)

## Not run: 
## Define the regions for multiple chrs
regs <- sapply(chrs, expressed_regions, project = "SRP002001", cutoff = 5L)

## You can then combine them into a single GRanges object if you want to
library("GenomicRanges")
single <- unlist(GRangesList(regs))

## End(Not run)

leekgroup/recount documentation built on May 24, 2024, 11:19 a.m.