coerceGR {derfinder} | R Documentation

## Coerce the coverage to a GRanges object for a given sample

### 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

[Package derfinder version 1.28.0 Index]