linkSet v0.99.3

The goal of linkSet is to provide tools for working with gene-enhancer interactions, which is commonly seen in HiC, PC-HiC, and single-cell ATAC-seq data analysis.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

linkSet is not currently available on Bioconductor. You can install it from GitHub with:

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("GilbertHan1011/linkSet")

Example

LinkSet can be converted from multiple data structures, like GRanges, GInteractions, and dataframes.

suppressMessages(library(linkSet))
## basic example code
library(GenomicRanges)
gr1 <- GRanges(seqnames = c("chr1", "chr1", "chr2"),
              ranges = IRanges(start = c(1, 100, 200), width = 10),
              strand = "+", symbol = c("Gene1", "Gene2", "Gene3"))
gr2 <- GRanges(seqnames = c("chr1", "chr2", "chr2"),
              ranges = IRanges(start = c(50, 150, 250), width = 10),
              strand = "+")
## construct linkSet
ls <- linkSet(gr1, gr2, specificCol = "symbol")
ls
#> linkSet object with 3 interactions and 1 metadata column:
#>              bait     seqnames_oe ranges_oe | anchor1.symbol
#>       <character>           <Rle> <IRanges> |    <character>
#>   [1]       Gene1 ---        chr1     50-59 |          Gene1
#>   [2]       Gene2 ---        chr2   150-159 |          Gene2
#>   [3]       Gene3 ---        chr2   250-259 |          Gene3
#>   -------
#>   regions: 6 ranges and 0 metadata columns
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths

The full manual can be reached at Documentation.