buildExpressionSummary {ENCODExplorer} | R Documentation

## Calculates average expression levels of the results of a previously completed ENCODE query.

### Description

This function takes the result of a previous call to `queryEncode`, splits the contained expression files by conditions (as specified by the `split_by` argument), then calculates average expression levels for each condition.

### Usage

    buildExpressionSummary(
      query_results,
      split_by,
      metric = NULL,
      simplify = FALSE,
      aggregate_function = mean,
      temp_dir = ".",
      force = FALSE
    )

### Arguments

`query_results` | A data.table returned by `queryEncode` or `queryEncodeGeneric`.
`split_by` | A vector of column names from query_results that will be used to split the average expression levels. If `NULL`, all elements of query_results are used in the same average expression calculation.
`metric` | A regular expression, indicating which column from the ENCODE data must be extracted. If NULL, ENCODExplorer data automatically detects and selects one of the TPM, FPKM or featurecount columns.
`simplify` | If TRUE, non-discriminatory columns are removed from the metadata, and if only one sample group is found, it is renamed "All".
`aggregate_function` | A function which takes a vector as input and returns a single value summarizing the whole. Used to summarize expression metrics.
`temp_dir` | The path to a directory where peak files will be downloaded.
`force` | A logical indicating whether already present files be redownloaded.

### Value

An object of class ENCODEExpressionSummary.

### Examples

    query_results = queryEncodeGeneric(biosample_name="neural tube",
                                       output_type="gene quantifications",
                                       file_type="tsv",
                                       assay="polyA plus RNA-seq",
                                       assembly="^mm10$",
                                       dataset_biosample_summary="(15.5|13.5)",
                                       fixed=FALSE)

    buildExpressionSummary(query_results, split_by="dataset_biosample_summary")

[Package ENCODExplorer version 2.13.1 Index]