Accessor for the sequencing coverage (read depth) matrix

Retrieves the sites × samples matrix of read depth from a commaData object.

Usage

# S4 method for class 'commaData'
coverage(x, shift = 0L, width = NULL, weight = 1L, ...)

Arguments

x

A commaData object.

shift

Not used; inherited from the IRanges::coverage generic.

width

Not used; inherited from the IRanges::coverage generic.

weight

Not used; inherited from the IRanges::coverage generic.

...

Not used.

Value

An integer matrix with rows corresponding to methylation sites and columns corresponding to samples.

See also

methylation, siteInfo

Examples

data(comma_example_data)
cov <- coverage(comma_example_data)
summary(as.vector(cov))
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#>   10.00   46.00   82.00   80.87  116.00  150.00