get_encode_peaks_metadata: Get ENCODE peaks metadata

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

Get ENCODE peaks metadata

Description

Get a subset of the ENCODE metadata for epigenomic peaks in human data.

Usage

get_encode_peaks_metadata(
  save_dir = tools::R_user_dir(package = "PeakyFinders", which = "cache"),
  overwrite = FALSE
)

Arguments

overwrite

Should any local files of the same name be overwritten? default TRUE.

Source

### Get peak data only ##### meta <- search_encode(file_type = "peak", assembly = "GRCh38", organism = "Homo sapiens", partial_match = TRUE) for(col in names(meta)){ if(all(is.na(meta[[col]]))){ messager("Removing:",col) meta[[col]] <- NULL } } tmp <- "~/Downloads/encode_peaks_metadata.tsv.gz" data.table::fwrite(meta, file = tmp, sep="\t") piggyback::pb_new_release(repo = "neurogenomics/PeakyFinders", tag="latest") piggyback::pb_upload(file = tmp, repo = "neurogenomics/PeakyFinders", overwrite = TRUE)

neurogenomics/PeakyFinders documentation built on March 24, 2024, 4:28 p.m.