search_encode: Search metadata: ENCODE

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

Search metadata: ENCODE

Description

Search metadata from the Encyclopedia of DNA Elements (ENCODE).

Usage

search_encode(
  assay = NULL,
  accession = NULL,
  file_accession = NULL,
  file_type = NULL,
  file_format = NULL,
  output_category = NULL,
  biosample_id = NULL,
  biosample_type = NULL,
  biosample_name = NULL,
  organism = NULL,
  dataset_type = NULL,
  assembly = NULL,
  genome_annotation = NULL,
  partial_match = TRUE,
  peaks_only = FALSE,
  verbose = TRUE,
  ...
)

Arguments

assay	Search "assay" column.
accession	Search "accession" column.
file_accession	Search "file_accession" column.
file_type	Search "file_type" column.
file_format	Search "file_format" column.
output_category	Search "output_category" column.
biosample_id	Search "biosample_id" column.
biosample_type	Search "biosample_type" column.
biosample_name	Search "biosample_name" column.
organism	Search "organism" column.
dataset_type	Search "dataset_type" column.
assembly	Search "assembly" column.
genome_annotation	Search "genome_annotation" column.
partial_match	Return case-insensitive substring matches instead of exact matches only (default: TRUE).
peaks_only	Return pre-filtered metadata for peak data aligned to the GRCh38 human genome build.
verbose	Print messages.
...	Additional metadata columns to filter.

Value

data.table.

Source

https://github.com/neurogenomics/EpiCompare/issues/43 Discussion on EpiCompare GitHub.

https://biodatascience.github.io/compbio/bioc/anno.html Mike Love tutorial on accessing peak data from AnnotationHub.

Examples

meta <- search_encode(assay = "chip-seq", 
                      biosample_name = "K562",
                      file_type = "peak",
                      assembly = "GRCh38",
                      organism = "Homo sapiens",
                      partial_match = TRUE)

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