Displays detailed information about a linkSet object, including regions, metadata, and optionally sequence information.
Usage
showLinkSet(
object,
margin = "",
print.seqinfo = FALSE,
print.classinfo = FALSE,
baitRegion = FALSE,
...
)
# S4 method for class 'linkSet'
showLinkSet(
object,
margin = "",
print.seqinfo = FALSE,
print.classinfo = FALSE,
baitRegion = FALSE
)Arguments
- object
A linkSet object to display
- margin
Character string for display margin (default: "")
- print.seqinfo
Logical, whether to print sequence information (default: FALSE)
- print.classinfo
Logical, whether to print class information (default: FALSE)
- baitRegion
Logical, whether to display bait regions (default: FALSE)
- ...
Additional arguments
Examples
gr1 <- GRanges(seqnames = c("chr1", "chr2", "chr3"),
ranges = IRanges(start = c(1000, 2000, 3000), width = 100),
strand = "+", symbol = c("BRCA1", "TP53", "NONEXISTENT"))
gr2 <- GRanges(seqnames = c("chr1", "chr2", "chr3"),
ranges = IRanges(start = c(5000, 6000, 7000), width = 100),
strand = "+")
ls <- linkSet(gr1, gr2, specificCol = "symbol")
showLinkSet(ls)
#> linkSet object with 3 interactions and 1 metadata column:
#> bait seqnames_oe ranges_oe | anchor1.symbol
#> [1] BRCA1 --- chr1 5000-5099 | BRCA1
#> [2] TP53 --- chr2 6000-6099 | TP53
#> [3] NONEXISTENT --- chr3 7000-7099 | NONEXISTENT