Package 'GPlinksR'

Build Gene-Peak Network (Enhancer, Promoter, Closest)

Description

Build Gene-Peak Network (Enhancer, Promoter, Closest)

Usage

build_gp_links(pk, gn, ver = 19, enh_file = NULL)

Arguments

pk	Either: (1) A character vector of genomic coordinates ("chr1:1000-1200"), or (2) A data.frame containing peak coordinates with columns "chr","start","end" or a "PeakRegion" column ("chr1:1000-1200" style).
gn	Character vector of gene symbols (HGNC official symbols, e.g. "TP53", "FMNL2").
ver	Integer (17, 18, or 19) - PANTHER enhancer-gene link version.
enh_file	Optional local path to enhancer-gene link file (.tsv).

Value

A data.frame with columns: Peak, Gene, Src. Closest-gene mappings are based on distance from each peak to gene TSS.

Examples

data("gp_example_inputs", package = "GPlinksR")
data("gp_example_links", package = "GPlinksR")
pk <- gp_example_inputs$pk[seq_len(3)]
gn <- gp_example_inputs$gn[seq_len(4)]

head(gp_example_links)

if (interactive()) {
    gp <- build_gp_links(pk, gn)
    head(gp)
}

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Build Gene-Peak Links from MAE or SCE Input

Description

Wrapper around build_gp_links() that extracts peak coordinates and gene symbols from a MultiAssayExperiment or SingleCellExperiment, then runs the standard GPlinksR workflow.

Usage

build_gp_links_wrapper(
    x,
    peak_experiment = NULL,
    gene_experiment = NULL,
    peak_col = NULL,
    gene_col = NULL,
    ver = 19,
    enh_file = NULL
)

Arguments

x	A MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, or RangedSummarizedExperiment.
peak_experiment	For MultiAssayExperiment, the experiment name holding peak features. For SingleCellExperiment, the altExp() name holding peak features.
gene_experiment	For MultiAssayExperiment, the experiment name holding gene features. Ignored for SingleCellExperiment, where the main experiment is used for genes.
peak_col	Optional rowData() column containing peak coordinates in "chr:start-end" format.
gene_col	Optional rowData() column containing gene symbols.
ver	Integer (17, 18, or 19). PEREGRINE enhancer-gene link version.
enh_file	Optional local path to enhancer-gene link file (.tsv).

Details

Peak features are extracted from rowRanges(), rowData(), or row names. Gene symbols are extracted from rowData() or row names.

Value

A data.frame with columns returned by build_gp_links().

Examples

if (requireNamespace("SingleCellExperiment", quietly = TRUE) &&
    requireNamespace("SummarizedExperiment", quietly = TRUE)) {
    sce <- SingleCellExperiment::SingleCellExperiment(
        assays = list(counts = matrix(seq_len(12), nrow = 3)),
        rowData = S4Vectors::DataFrame(symbol = c("TP53", "GATA1", "SPI1"))
    )

    SingleCellExperiment::altExp(sce, "ATAC") <-
        SummarizedExperiment::SummarizedExperiment(
            assays = list(counts = matrix(seq_len(12), nrow = 3)),
            rowData = S4Vectors::DataFrame(
                PeakRegion = c(
                    "chr1:1000-1200",
                    "chr1:5000-5200",
                    "chr2:9000-9300"
                )
            )
        )

    sce
    # Example wrapper call:
    # build_gp_links_wrapper(
    #     x = sce, peak_experiment = "ATAC", gene_col = "symbol"
    # )
}

---

Download Enhancer-Gene Link File from PANTHER Peregrine Database

Description

Download Enhancer-Gene Link File from PANTHER Peregrine Database

Usage

get_peregrine_file(version = 19)

Arguments

version

Integer (17, 18, or 19). Which PANTHER enhancer-gene link version to download.

Value

The full path to the downloaded .tsv file stored in the BiocFileCache.

Examples

if (interactive()) {
    f <- get_peregrine_file(19)
    f
    readLines(f, n = 3)
}

---

Example Gene and Peak Inputs for GPlinksR

Description

A small example dataset for demonstrating GPlinksR workflows. The object contains 300 peak coordinates and 100 gene symbols suitable for examples and vignettes. The first few entries are curated so that the vignette examples produce enhancer-, promoter-, and closest-based links from the packaged data.

Usage

data(gp_example_inputs)

Format

A list with two elements:

pk

A character vector of 300 peak coordinates in "chr:start-end" format.

gn

A character vector of 100 gene symbols.

Examples

data(gp_example_inputs)
length(gp_example_inputs$pk)
length(gp_example_inputs$gn)

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Example Link Table for the Packaged GPlinksR Demo Subset

Description

A precomputed example gene-peak link table corresponding to the curated leading entries in gp_example_inputs. The table includes enhancer-, promoter-, and closest-based links and is used in the vignette to display representative output without rerunning external downloads.

Usage

data(gp_example_links)

Format

A data.frame with 7 rows and 3 columns:

Peak

Peak coordinate in "chr:start-end" format.

Gene

Gene symbol linked to the peak.

Src

Link source, one of "enh", "prom", or "clo".

Examples

data(gp_example_links)
head(gp_example_links)
table(gp_example_links$Src)

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