search_roadmap: 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_roadmap(
  output_category = NULL,
  output_type = NULL,
  file_format_type = NULL,
  biosample_id = NULL,
  biosample_type = NULL,
  biosample_name = NULL,
  dataset_biosample_summary = NULL,
  dataprovider = NULL,
  species = NULL,
  genome = NULL,
  description = NULL,
  rdataclass = NULL,
  sourcetype = NULL,
  partial_match = TRUE,
  peaks_only = FALSE,
  verbose = TRUE,
  ...
)

Arguments

output_category	Search "output_category" column.
output_type	Search "output_type" column.
file_format_type	Search "file_format_type" column.
biosample_id	Search "biosample_id" column.
biosample_type	Search "biosample_type" column.
biosample_name	Search "biosample_name" column.
dataset_biosample_summary	Search "dataset_biosample_summary" column.
dataprovider	Search "dataprovider" column.
species	Search "species" column.
genome	Search "genome" column.
description	Search "description" column.
rdataclass	Search "rdataclass" column.
sourcetype	Search "sourcetype" 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 metdata 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_roadmap(biosample_type="brain",
                       file_format_type="narrowPeak",
                       genome="hg19",
                       peaks_only=TRUE)

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