getENCODEdata: Download enhancer sequences from ENCODE

In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

Download enhancer sequences from ENCODE

Description

Query enhancer peak and extract sequences from ENCODE

Usage

getENCODEdata(
  genome,
  markers = "H3K4me1",
  window_size = 1000L,
  step = 50L,
  output = c("Enhancer", "raw_peaks"),
  ...
)

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.
output	Output format. If it is 'raw_peaks', the raw peaks list will be returned. Otherwise, the Enhancer object will be returned.
...	Parameters can be passed to queryEncode

Value

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

Examples

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

jianhong/enhancerHomologSearch documentation built on Nov. 19, 2024, 11:13 p.m.