queryEncode {ENCODExplorer} | R Documentation

## 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 = 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.frame`s containing data about ENCODE experiments and datasets

### Examples

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

[Package ENCODExplorer version 2.13.1 Index]