get_chromHMM_annotation: Download ChromHMM annotation file(s)

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

Download ChromHMM annotation file(s)

Description

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.

Usage

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.

neurogenomics/EpiCompare documentation built on April 30, 2024, 3:58 p.m.