buildExpressionSummary {ENCODExplorer} | R Documentation |
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.
buildExpressionSummary( query_results, split_by, metric = NULL, simplify = FALSE, aggregate_function = mean, temp_dir = ".", force = FALSE )
query_results |
A data.table returned by |
split_by |
A vector of column names from query_results that will be used
to split the average expression levels.
If |
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. |
An object of class ENCODEExpressionSummary.
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")