gtrack.liftover: Imports a track from another assembly

In misha: Toolkit for Analysis of Genomic Data

Imports a track from another assembly

Description

Imports a track from another assembly.

Usage

gtrack.liftover(
  track = NULL,
  description = NULL,
  src.track.dir = NULL,
  chain = NULL,
  src_overlap_policy = "error",
  tgt_overlap_policy = "auto",
  multi_target_agg = c("mean", "median", "sum", "min", "max", "count", "first", "last",
    "nth", "max.coverage_len", "min.coverage_len", "max.coverage_frac",
    "min.coverage_frac"),
  params = NULL,
  na.rm = TRUE,
  min_n = NULL,
  min_score = NULL
)

Arguments

track	name of a created track
description	a character string description
src.track.dir	path to the directory of the source track
chain	name of chain file or data frame as returned by 'gintervals.load_chain'
src_overlap_policy	policy for handling source overlaps: "error" (default), "keep", or "discard". "keep" allows one source interval to map to multiple target intervals, "discard" discards all source intervals that have overlaps and "error" throws an error if source overlaps are detected.
tgt_overlap_policy	policy for handling target overlaps. One of: Policy Description error Throws an error if any target overlaps are detected. auto Default. Alias for "auto_score". auto_score Resolves overlaps by segmenting the target region and selecting the best chain for each segment based on alignment score (highest score wins). Tie-breakers: longest span, then lowest chain_id. auto_longer Resolves overlaps by segmenting and selecting the chain with the longest span for each segment. Tie-breakers: highest score, then lowest chain_id. auto_first Resolves overlaps by segmenting and selecting the chain with the lowest chain_id for each segment. keep Preserves all overlapping intervals. discard Discards any chain interval that has a target overlap with another chain interval. agg Segments overlaps into smaller disjoint regions where each region contains all contributing chains, allowing downstream aggregation to process multiple values per region. best_source_cluster Best source cluster strategy based on source overlap. When multiple chains map a source interval, clusters them by source overlap: if chain source intervals overlap (indicating true duplications), all mappings are retained; if chain source intervals are disjoint (indicating conflicting/alternative mappings), only the cluster with the largest total target length is kept.
multi_target_agg	aggregation/selection policy for contributors that land on the same target locus. When multiple source intervals map to overlapping regions in the target genome (after applying tgt_overlap_policy), their values must be combined into a single value.
params	additional parameters for aggregation (e.g., for "nth" aggregation)
na.rm	logical indicating whether NA values should be removed before aggregation (default: TRUE)
min_n	minimum number of non-NA values required for aggregation. If fewer values are available, the result will be NA.
min_score	optional minimum alignment score threshold. Chains with scores below this value are filtered out. Useful for excluding low-quality alignments.

Details

This function imports a track located in 'src.track.dir' of another assembly to the current database. 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 name of the newly created track is specified by 'track' argument and 'description' is added as a track attribute.

Note: When passing a pre-loaded chain (data frame), overlap policies cannot be specified - they are taken from the chain's attributes that were set during loading. When passing a chain file path, policies can be specified and will be used for loading. Aggregation parameters (multi_target_agg, params, na.rm, min_n) can always be specified regardless of chain type.

Value

None.

Note

Terminology note for UCSC chain format users: In the UCSC chain format specification, the fields prefixed with 't' (tName, tStart, tEnd, etc.) are called "target" or "reference", while fields prefixed with 'q' (qName, qStart, qEnd, etc.) are called "query". However, misha uses reversed terminology: UCSC's "target/reference" corresponds to misha's "source" (chromsrc, startsrc, endsrc), and UCSC's "query" corresponds to misha's "target" (chrom, start, end).

See Also

gintervals.load_chain, gintervals.liftover

misha documentation built on Dec. 14, 2025, 9:06 a.m.