Subset a commaData object by condition, modification type, or chromosome

A convenience function for filtering a commaData object by common criteria. For arbitrary index-based subsetting, use [.

Usage

subset(x, ...)

# S4 method for class 'commaData'
subset(x, mod_type = NULL, condition = NULL, chrom = NULL, ...)

Arguments

x

A commaData object.

...

Ignored.

mod_type

Character vector or NULL. If provided, only sites with a matching modification type are kept (e.g., "6mA").

condition

Character vector or NULL. If provided, only samples matching the specified condition(s) are kept.

chrom

Character vector or NULL. If provided, only sites on the specified chromosome(s) are kept.

Value

A commaData object containing only the selected sites and samples.

Examples

data(comma_example_data)
# Only 6mA sites
six_ma <- subset(comma_example_data, mod_type = "6mA")
modTypes(six_ma)
#> [1] "6mA"