createDesign {ENCODExplorer} | R Documentation

## Create a design for the files associated with the result of a queryEncode, fuzzySearch research or a `data.table` from createDesign.

### Description

Create a design for the files associated with the result of a queryEncode, fuzzySearch research or a `data.table` from createDesign.

### Usage

    createDesign(
      input = NULL,
      df = get_encode_df(),
      split = FALSE,
      fileFormat = "bam",
      dataset_type = "experiments",
      format = "long",
      output_type = "data.table",
      ID = c(1, 2)
    )

### Arguments

`input` | The `data.table` created by a queryEncode or searchEncode research, or a
`df` | The `data.table` used to extract the files link. Default :`get_encode_df()`
`split` | Allow to the function to return a `list` of `data.table` where each `data.table` contain the files for a single experiment Default: `FALSE`.
`fileFormat` | A string that correspond to the type of the files that need to be extracted. Default: bam
`dataset_type` | A string that correspong to the type of dataset that will be extrated. Default: experiments
`format` | The format (long or wide) to represent the data. The 'long' format will contain three columns (File, Experiment, Value). The 'wide' format organize the data as an array with the experiments as columns and files as rows. Default: long
`output_type` | The type of output of the function, can be `data.table` or a `data.table` Default: `data.table`
`ID` | A two element numeric vector, that first element is the value assign to replicate and the second is the value assign to control. Default: 1 and 2

### Value

is a `data.table` with files for all the experiments or a `list` of `data.table` with all the file per experiment when the parameter split is set to `TRUE`

### Examples

    # You will need to replace get_encode_df_demo() with your own encode_df object,
    # the get_encode_df() function or the get_encode_df_full() function.
    fuzzy_result <- fuzzySearch(searchTerm = "brca",
    database=get_encode_df_demo(), filterVector ="target")
    design_result <- createDesign(input = fuzzy_result,df=get_encode_df_demo(),
    fileFormat="fastq")

[Package ENCODExplorer version 2.14.0 Index]