misha (version 4.2.9)

gintervals.liftover: Converts intervals from another assembly

Description

Converts intervals from another assembly to the current one.

Usage

gintervals.liftover(intervals = NULL, chain = NULL)

Value

A data frame representing the converted intervals.

Arguments

intervals

intervals from another assembly

chain

name of chain file or data frame as returned by 'gintervals.load_chain'

Details

This function converts 'intervals' from another assembly to the current one. Chain file instructs how the conversion of coordinates should be done. It can be either a name of a chain file or a data frame in the same format as returned by 'gintervals.load_chain' function.

The converted intervals are returned. An additional column named 'intervalID' is added to the resulted data frame. For each interval in the resulted intervals it indicates the index of the original interval.

See Also

gintervals.load_chain, gtrack.liftover, gintervals

Examples

# \dontshow{
options(gmax.processes = 2)
# }

gdb.init_examples()
chainfile <- paste(.misha$GROOT, "data/test.chain", sep = "/")
intervs <- data.frame(
    chrom = "chr25", start = c(0, 7000),
    end = c(6000, 20000)
)
gintervals.liftover(intervs, chainfile)