queryGeneExpression: Queries and returns average gene expression level for a given...

In ENCODExplorer: A compilation of ENCODE metadata

Description

ENCODE files are automatically split by biosample_description (which will separate samples from different cell fractions or sequencing methods) and by the treatment columns.

Usage

queryGeneExpression(
  biosample_name,
  assay = NULL,
  assembly = NULL,
  simplify = TRUE,
  use_interactive = FALSE
)

Arguments

biosample_name	The cell-line/tissue for which average expression levels should be queried.
assay	The assay type to summarize. If NULL, the most generic assay type is automatically selected.
assembly	The target genomic assembly. If NULL, the most recent available assembly is selected.
simplify	If TRUE, non-discriminatory columns are removed from the metadata, and if only one sample group is found, it is renamed "All".
use_interactive	If TRUE, the user will be prompted to select prefered metadata values when multiple possibilities are available. available assembly is selected.

Value

An object of class ENCODEExpressionSummary.

See Also

buildExpressionSummary, queryTranscriptExpression

Examples

  queryGeneExpression("bone marrow")

ENCODExplorer documentation built on Nov. 8, 2020, 5:11 p.m.