GitHub - GilbertHan1011/linkSet (original) (raw)

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 #> | #> [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 atDocumentation.