gintervals.liftover {misha} | R Documentation |
Converts intervals from another assembly
Description
Converts intervals from another assembly to the current one.
Usage
gintervals.liftover(intervals = NULL, chain = NULL)
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.
Value
A data frame representing the converted intervals.
See Also
gintervals.load_chain
, gtrack.liftover
,
gintervals
Examples
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)
[Package misha version 4.3.6 Index]