Transforms existing intervals to a chain format

Transforms existing intervals to a chain format by validating required columns and adding chain attributes.

gintervals.as_chain(
  intervals = NULL,
  src_overlap_policy = "error",
  tgt_overlap_policy = "auto",
  min_score = NULL
)

Arguments

intervals

a data frame with chain columns: chrom, start, end, strand, chromsrc, startsrc, endsrc, strandsrc, chain_id, score

src_overlap_policy

source overlap policy: "error", "keep", or "discard"

tgt_overlap_policy

target overlap policy: "error", "auto", "auto_first", "auto_longer", "auto_score", "discard", "keep", or "agg"

min_score

optional minimum alignment score threshold

Value

A data frame in chain format with chain attributes set

Details

This function checks that the input intervals data frame has all the required columns for a chain format and adds the necessary attributes. A chain format requires both target coordinates (chrom, start, end, strand) and source coordinates (chromsrc, startsrc, endsrc, strandsrc), as well as chain_id and score columns.

See also

gintervals.load_chain, gintervals.liftover

Examples

gdb.init_examples()

# Create a chain from existing intervals
chain_data <- data.frame(
    chrom = "chr1",
    start = 1000,
    end = 2000,
    strand = 0,
    chromsrc = "chr1",
    startsrc = 5000,
    endsrc = 6000,
    strandsrc = 0,
    chain_id = 1L,
    score = 1000.0
)
chain <- gintervals.as_chain(chain_data)