Download enhancer sequences from ENCODE — getENCODEdata • enhancerHomologSearch

Query enhancer peak and extract sequences from ENCODE

getENCODEdata(
  genome,
  markers = "H3K4me1",
  window_size = 1000L,
  step = 50L,
  ...
)

Arguments

genome: An object of BSgenome.
markers: Enhancer markers. Default 'H3K4me1'. For active enhancer, it can be set as c('H3K4me1', 'H3K27ac'). If markers is a `GRanges` object, the function will skip the download step.
window_size, step: The size of windows and steps to split the peaks into small pieces. These parameter is used because the width of histone marker peaks are different sizes. Break the peaks into small pieces can increase the matching score and align the matching for different peaks into same size. The window_size is also be used for overlapping detection of multiple histone markers.
...: Parameters can be passed to queryEncode

An object of Enhancers with genome, and peaks. The peaks is an object of GRanges. The genome is an object of BSgenome.

library(BSgenome.Hsapiens.UCSC.hg38)
hs <- getENCODEdata(genome=Hsapiens,
                    partialMatch=c(biosample_summary="spinal cord"))