ENCODExplorer (version 1.4.3)

queryEncode: Produce a subset of data following predefined criteria

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 = NULL, set_accession = NULL, assay = NULL, biosample = NULL, dataset_accession = NULL, file_accession = NULL, file_format = NULL, lab = NULL, organism = NULL, target = NULL, treatment = NULL, project = NULL, file_status = "released", status = "released", fixed = TRUE, quiet = FALSE)

Arguments

df

list of two data.frame containing ENCODE experiment and dataset metadata

set_accession

character string to select the experiment or dataset accession

assay

character string to select the assay type

biosample

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

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.

Value

a list of two data.frames containing data about ENCODE experiments and datasets

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

Examples

    queryEncode(biosample = "A549", file_format = "bam")