queryEncode: Produce a subset of data following predefined criteria

In CharlesJB/ENCODExplorer: A compilation of ENCODE metadata

Description

After running the prepare_ENCODEDb function, this function will allow you to extract a subset of data encording to the following criteria : accession, assay name, biosample, dataset accession, file accession, file format, laboratory, donor organism, target and treatment.

Usage

queryEncode(
  df = get_encode_df(),
  set_accession = NULL,
  assay = NULL,
  biosample_name = NULL,
  dataset_accession = NULL,
  file_accession = NULL,
  file_format = NULL,
  lab = NULL,
  organism = NULL,
  target = NULL,
  treatment = NULL,
  project = NULL,
  biosample_type = NULL,
  file_status = "released",
  status = "released",
  fixed = TRUE,
  quiet = FALSE,
  fuzzy = FALSE
)

Arguments

df	data.frame containing ENCODE experiment and dataset metadata
set_accession	character string to select the accession
assay	character string to select the assay type
biosample_name	character string to select the biosample name
dataset_accession	character string to select the dataset accession
file_accession	character string to select the file accesion
file_format	character string to select the file format
lab	character string to select the laboratory
organism	character string to select the donor organism
target	character string to select the experimental target
treatment	character string to select the treatment
project	character string to select the project
biosample_type	character string to select the biosample type
file_status	character string to select the file status ("released", "revoked", "all"). Default "released"
status	character string to select the dataset/experiment status
fixed	logical. If TRUE, pattern is a string to be matched as it is.
quiet	logical enables to switch off the result summary information when setting at TRUE.
fuzzy	Search for substring or alternate hyphenations. Default: TRUE

Details

By default, the query can be made on an exact match term. This behaviour can be modified by setting the fixed argument at TRUE

Value

a data.frames containing data about ENCODE experiments and datasets

Examples

    queryEncode(df = get_encode_df_demo(), biosample_name = "A549",
                file_format = "bam")

CharlesJB/ENCODExplorer documentation built on Dec. 9, 2019, 10:11 a.m.