Import genomic interactions from URL — importGInteractionsFromUrl • geomeTriD.documentation

Download files and import interactions

importGInteractionsFromUrl(
  urls,
  resolution,
  range,
  format = "cool",
  normalization = "balanced"
)

Arguments

urls: Vector of character. URLs.
resolution: The resolution of the matrix.
range: GRanges object. The coordinates.
format: The format of the file.
normalization: Normalization matrix in the file.

Value

A list of GInteractions object

Examples

library(GenomicRanges)
range_chr8<- GRanges('chr8:85550000-85800000')
url <- paste0("https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6281nnn/",
 "GSM6281851/suppl/GSM6281851_RCMC_BR1_merged_allCap_DMSO_mm39.merged.50.mcool")
gi <- importGInteractionsFromUrl(urls=url, resolution=500, range=range_chr8,
                                 format='cool', normalization='balanced')