Loads assembly conversion table from a chain file

Loads assembly conversion table from a chain file.

gintervals.load_chain(file = NULL)

Arguments

file

name of chain file

Value

A data frame representing assembly conversion table.

Details

This function reads a file in 'chain' format and returns assembly conversion table that can be used in 'gtrack.liftover' and 'gintervals.liftover'.

Note: chain file might map a few different source intervals into a single target one. These ambiguous mappings are not presented in the data frame returned by 'gintervals.load_chain'.

See also

gintervals.liftover, gtrack.liftover

Examples

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

gdb.init_examples()
chainfile <- paste(.misha$GROOT, "data/test.chain", sep = "/")
gintervals.load_chain(chainfile)
#>   chrom start   end chromsrc startsrc
#> 1  chr1 12700 13500    chr25     2500
#> 2  chr1 14100 18500    chr25     3600
#> 3  chrX  5000  7000    chr25    10000