queryTranscriptExpression: Queries and returns average transcript expression level for a...

In CharlesJB/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

queryTranscriptExpression(
  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.

Value

An object of class ENCODEExpressionSummary.

See Also

buildExpressionSummary, queryGeneExpression

Examples

  queryTranscriptExpression("bone marrow")

CharlesJB/ENCODExplorer documentation built on Dec. 9, 2019, 10:11 a.m.