Download ChromHMM annotation file(s)

Source: R/get_chromHMM_annotation.R

Download ChromHMM annotation file(s) for a given cell-line (returned as a GRanges object) or a list of cell-lines (returned as a named list of GRanges objects). All annotations are aligned to the hg19 genome build. All data can be found on the UCSC Genome Browser here.

get_chromHMM_annotation(
  cell_line,
  cache = BiocFileCache::BiocFileCache(ask = FALSE)
)

Arguments

cell_line

ChromHMM annotation for user-specified cell-line. Cell-line options are:

  • "K562" = K-562 cells

  • "Gm12878" = Cellosaurus cell-line GM12878

  • "H1hesc" = H1 Human Embryonic Stem Cell

  • "Hepg2" = Hep G2 cell

  • "Hmec" = Human Mammary Epithelial Cell

  • "Hsmm" = Human Skeletal Muscle Myoblasts

  • "Huvec" = Human Umbilical Vein Endothelial Cells

  • "Nhek" = Normal Human Epidermal Keratinocytes

  • "Nhlf" = Normal Human Lung Fibroblasts

Value

Cell-line specific ChromHMM annotation file. Default K562 cell-line.