exportInteractTrack: Export predicted gene-pair interaction

In rliger: Linked Inference of Genomic Experimental Relationships

Export predicted gene-pair interaction

Description

Export the predicted gene-pair interactions calculated by upstream function linkGenesAndPeaks into an Interact Track file which is compatible with UCSC Genome Browser.

Usage

exportInteractTrack(
  corrMat,
  pathToCoords,
  useGenes = NULL,
  outputPath = getwd()
)

Arguments

corrMat	A sparse matrix of correlation with peak names as rows and gene names as columns.
pathToCoords	Path to the gene coordinates file.
useGenes	Character vector of gene names to be exported. Default NULL uses all genes available in corrMat.
outputPath	Path of filename where the output file will be stored. If a folder, a file named "Interact_Track.bed" will be created. Default current working directory.

Value

No return value. A file located at outputPath will be created.

Examples

bmmc <- normalize(bmmc)
bmmc <- selectGenes(bmmc)
bmmc <- scaleNotCenter(bmmc)
if (requireNamespace("RcppPlanc", quietly = TRUE) &&
    requireNamespace("GenomicRanges", quietly = TRUE) &&
    requireNamespace("IRanges", quietly = TRUE) &&
    requireNamespace("psych", quietly = TRUE)) {
    bmmc <- runINMF(bmmc)
    bmmc <- alignFactors(bmmc)
    bmmc <- normalizePeak(bmmc)
    bmmc <- imputeKNN(bmmc, reference = "atac", queries = "rna")
    corr <- linkGenesAndPeaks(
        bmmc, useDataset = "rna",
        pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger")
    )
    resultPath <- tempfile()
    exportInteractTrack(
        corrMat = corr,
        pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger"),
        outputPath = resultPath
    )
    head(read.table(resultPath, skip = 1))
}

rliger documentation built on Oct. 30, 2024, 1:07 a.m.