import_peaks_encode: Import peaks: ENCODE
In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

import_peaks_encode

R Documentation

Import peaks: ENCODE

Description

Import peaks from the Encyclopedia of DNA Elements (ENCODE).

Usage

import_peaks_encode(
  ids,
  build = "hg19",
  query_granges = NULL,
  query_granges_build = NULL,
  split_chromosomes = FALSE,
  condense_queries = TRUE,
  force_new = FALSE,
  method = "MACSr",
  cutoff = NULL,
  searches = construct_searches(),
  peaks_dir = tempdir(),
  nThread = 1,
  verbose = TRUE
)

Arguments

`ids`	IDs from one of the supported databases. IDs can be at any level: file, sample, or experiment.
`query_granges`	[Optional] GRanges object indicating which genomic regions to extract from each sample.
`query_granges_build`	[Optional] Genome build that `query_granges` is aligned to.
`split_chromosomes`	Split single-threaded query into multi-threaded query across chromosomes. This is can be helpful especially when calling peaks from large bigWig/bedGraph files. The number of threads used is set by the `nThread` argument.
`condense_queries`	Condense `query_granges` by taking the min/max position per chromosome (default: `TRUE)`. This helps to reduce the total number of queries, which can cause memory allocation problems due to repeated calls to the underlying C libraries.
`force_new`	By default, saved results of the same `save_path` name will be imported instead of running queries. However you can override this by setting `force_new` to perform new queries regardless and overwrite the old `save_path` file.
`method`	Method to call peaks with: "MACSr" : Uses MACS3 via bdgpeakcall. "SEACR" : Uses SEACR via find_packages.
`cutoff`	when `method="MACSr"` : Passed to `cutoff` argument. Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS3, score 5 means pvalue 1e-5. If `NULL`, a reasonable `cutoff` value will be inferred through a `cutoff_analysis`. when `method="SEACR"` : Passed to `control` argument. Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. Alternatively, a numeric threshold n between 0 and 1 returns the top n fraction of peaks based on total signal within peaks (default: `0.05`).
`searches`	Named list of regex queries.
`peaks_dir`	Directory to save peaks to (only used when calling peaks from bedGraph files).
`nThread`	When `nThread>1`, accelerates file importing and peak calling using multi-core parallelisation.
`verbose`	Print messages.