convertToTargetRegions: convertToTargetRegions

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

convertToTargetRegions

Description

Convert a set of input regions to the overlapping regions in the target set.

Usage

convertToTargetRegions(
  queryRegions,
  targetRegions,
  minOverlap = 0.4,
  overlapType = "any",
  returnCorrespondence = FALSE,
  verbose = TRUE
)

Arguments

queryRegions	List of regions to convert (normally the query region set).
targetRegions	List of regions in the target set (normally the database).
minOverlap	Minimum overlap to consider (in either direction, default: 0.40).
overlapType	Parameter for findOverlaps (default: "any")
returnCorrespondence	Returns a table containing the matches, or only a list of overlapping regions (default: FALSE).
verbose	Print the number of regions selected?

Value

IDs of the regions in the "target regions" overlapping with the query regions.

See Also

getDbRegionsLoc.

See the package vignette for examples and more details: vignette("RcisTarget")

Examples

## Not run: 
 ## To apply on a list of regionSets:
 regionSets_db <- lapply(regionSets, function(x) 
    convertToTargetRegions(queryRegions=x, targetRegions=dbRegionsLoc))
 
## End(Not run)

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.