The linkSet package provides tools for working with genomic link sets, which represent connections between different genomic regions. This package is designed for bioinformatics and genomic data analysis, offering various methods to manipulate and analyze linkSet objects.
Details
The main class provided by this package is the linkSet class, which is
designed to represent and analyze genomic interactions, particularly
focusing on gene-enhancer relationships. Key features include:
Representation of genomic interactions with two types of anchors: "bait" (typically genes) and "other end" (typically enhancers or other regulatory elements).
Flexible input methods, supporting construction from various data types.
Metadata storage for additional information about interactions.
Integration with Bioconductor classes and tools.
Methods for annotating promoters and distinguishing between inter- and intra-chromosomal interactions.
Examples
data(linkExample)
linkExample
#> linkSet object with 5 interactions and 1 metadata column:
#> bait seqnames_oe ranges_oe | anchor1.symbol
#> <character> <Rle> <IRanges> | <character>
#> [1] Gene1 --- chr1 50-59 | Gene1
#> [2] Gene1 --- chr2 150-159 | Gene1
#> [3] Gene2 --- chr2 250-259 | Gene2
#> [4] Gene3 --- chr4 350-359 | Gene3
#> [5] Gene3 --- chr4 450-459 | Gene3
#> -------
#> regions: 10 ranges and 0 metadata columns
#> seqinfo: 4 sequences from an unspecified genome; no seqlengths