peaks_metadata_encode: Get ENCODE peaks metadata

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

Get ENCODE peaks metadata

Description

A subset of the ENCODE metadata that includes links to all human epigenomic peaks data.

Usage

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

Arguments

save_dir	Directory to cache file in.
overwrite	Should any local files of the same name be overwritten? default TRUE.

Value

data.table.

Source

### Get peak data only ##### meta <- search_encode(file_type = c("^bed narrowpeak","^bed broadpeak"), assembly = "GRCh38", organism = "Homo sapiens", partial_match = TRUE) meta <- subset(meta[(!file_type PeakyFinders:::drop_empty_cols(meta) tmp <- "~/Downloads/encode_peaks_metadata.tsv.gz" data.table::fwrite(meta, file = tmp, sep="\t")

Examples

meta <- peaks_metadata_encode()

neurogenomics/PeakyFinders documentation built on Oct. 14, 2024, 3:09 p.m.