queryTranscriptExpression {ENCODExplorer}R Documentation

Queries and returns average transcript expression level for a given biosample_name.

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")

[Package ENCODExplorer version 2.12.1 Index]