queryExpressionGeneric: Queries and returns average expression levels 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

queryExpressionGeneric(
  biosample_name,
  level = "gene quantifications",
  assay = NULL,
  assembly = NULL,
  simplify = TRUE,
  use_interactive = FALSE
)

Arguments

biosample_name	The cell-line/tissue for which average expression levels should be queried.
level	The type of expression level to summarize, either "gene quantifications" or "transcript quantifications".
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

  queryExpressionGeneric("bone marrow")

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