coerceGR: Coerce the coverage to a GRanges object for a given sample

In derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Description

Given the output of fullCoverage, coerce the coverage to a GRanges object.

Usage

coerceGR(sample, fullCov, ...)

Arguments

sample	The name or integer index of the sample of interest to coerce to a GRanges object.
fullCov	A list where each element is the result from loadCoverage used with returnCoverage = TRUE. Can be generated using fullCoverage.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If TRUE basic status updates will be printed along the way. seqlengths A named vector with the sequence lengths of the chromosomes. This argument is passed to GRanges. By default this is NULL and inferred from the data. Passed to define_cluster.

Value

A GRanges object with score metadata vector containing the coverage information for the specified sample. The ranges reported are only those for regions of the genome with coverage greater than zero.

Author(s)

Leonardo Collado-Torres

See Also

GRanges

Examples

## Create a small fullCov object with data only for chr21
fullCov <- list("chr21" = genomeDataRaw)

## Coerce to a GRanges the first sample
gr <- createBwSample("ERR009101",
    fullCov = fullCov,
    seqlengths = c("chr21" = 48129895)
)

## Explore the output
gr


## Coerces fullCoverage() output to GRanges for a given sample

derfinder documentation built on Dec. 20, 2020, 2 a.m.