Display detailed information about a linkSet object

Usage

# S4 method for class 'linkSet'
show(object)

# S4 method for class 'linkSet'
showLinkSet(
  x,
  margin = "",
  print.seqinfo = FALSE,
  print.classinfo = FALSE,
  baitRegion = FALSE
)

Examples

# Example usage of show method for linkSet object
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")
show(ls)
#> linkSet object with 3 interactions and 1 metadata column:
#>              bait     seqnames_oe ranges_oe | anchor1.symbol
#>       <character>           <Rle> <IRanges> |    <character>
#>   [1]       BRCA1 ---        chr1 5000-5099 |          BRCA1
#>   [2]        TP53 ---        chr2 6000-6099 |           TP53
#>   [3] NONEXISTENT ---        chr3 7000-7099 |    NONEXISTENT
#>   -------
#>   regions: 6 ranges and 0 metadata columns
#>   seqinfo: 3 sequences from an unspecified genome; no seqlengths
# Example usage of showLinkSet method for linkSet object
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